Publikacje

Publikacje Pracowni Modelowania Molekularnego

  • 2022
  • Biskupek Iga, Czaplewski Cezary, Sawicka Justyna, Iłowska Emilia, Dzierżyńska Maria, Rodziewicz-Motowidło Sylwia, Liwo Józef Adam: Prediction of aggregation of biologically-active peptides with the UNRES coarse-grained model, Biomolecules, 2022, vol. 12, nr 8, s.1-18, Numer artykułu:1140. DOI:10.3390/biom12081140
  • Biskupek Iga, Sieradzan Adam, Czaplewski Cezary, Liwo Józef Adam, Lesner Adam, Giełdoń Artur: Theoretical investigation of the coronavirus SARS-CoV-2 (COVID-19) infection mechanism and selectivity, Molecules, 2022, vol. 27, nr 7, s.1-11, Numer artykułu:2080. DOI:10.3390/molecules27072080
  • Bogunia  Małgorzata, Liwo Józef Adam, Czaplewski Cezary, Makowska Joanna, Giełdoń Artur, Makowski Mariusz: Influence of temperature and salt concentration on the hydrophobic interactions of adamantane and hexane, Journal of Physical Chemistry B, 2022, vol. 126, nr 3, s.634-642. DOI:10.1021/acs.jpcb.1c09860
  • Bojarski Krzysztof, Sage J., Samsonov Sergey [i in.]: In silico and in vitro mapping of specificity patterns of glycosaminoglycans towards cysteine cathepsins B, L, K, S and V, Journal of Molecular Graphics & Modelling, 2022, vol. 113, s.1-10, Numer artykułu:108153. DOI:10.1016/j.jmgm.2022.108153
  • Bojko Magdalena, Węgrzyn Katarzyna, Sikorska Emilia, Kocikowski Mikołaj, Kogut Małgorzata, Sieradzan Adam, Spodzieja Marta, Rodziewicz-Motowidło Sylwia [i in.]: Design, synthesis and biological evaluation of PD-1 derived peptides as inhibitors of PD-1/PD-L1 complex formation for cancer therapy, Bioorganic Chemistry, 2022, vol. 128, s.1-15, Numer artykułu:106047. DOI:10.1016/j.bioorg.2022.106047
  • Danielsson Annemarie, Kogut Małgorzata, Maszota-Zieleniak Martyna, Samsonov Sergey [i in.]: Molecular dynamics-based descriptors of 3-O-Sulfated Heparan sulfate as contributors of protein binding specificity, Computational Biology and Chemistry, 2022, vol. 99, s.1-14, Numer artykułu:107716. DOI:10.1016/j.compbiolchem.2022.107716
  • de Carvalho Bertozo Luiza, Kogut Małgorzata, Maszota-Zieleniak Martyna, Samsonov Sergey [i in.]: Induced circular dichroism as a tool to monitor the displacement of ligands between albumins, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2022, vol. 278, s.1-13, Numer artykułu:121374. DOI:10.1016/j.saa.2022.121374
  • Denamur Sophie, Maszota-Zieleniak Martyna, Samsonov Sergey [i in.]: Binding of heparan sulfate to human cystatin C modulates inhibition of cathepsin L: putative consequences in mucopolysaccharidosis, Carbohydrate Polymers, 2022, vol. 293, s.1-12, Numer artykułu:119734. DOI:10.1016/j.carbpol.2022.119734
  • Giatagana Eirini-Maria, Gaardløs Margrethe , Samsonov Sergey [i in.]: Biglycan interacts with type I insulin-like receptor (IGF-IR) signaling pathway to regulate osteosarcoma cell growth and response to chemotherapy, Cancers, 2022, vol. 14, nr 5, s.1-25, Numer artykułu:1196. DOI:10.3390/cancers14051196
  • Kogut Małgorzata, Grabowska Ola, Wyrzykowski Dariusz, Samsonov Sergey: Affinity and putative entrance mechanisms of alkyl sulfates into the β-CD cavity, Journal of Molecular Liquids, 2022, vol. 364, s.1-11, Numer artykułu:119978. DOI:10.1016/j.molliq.2022.119978
  • Kogut Małgorzata, Danielsson Annemarie, Samsonov Sergey [i in.]: Impact of calcium ions on the structural and dynamic properties of heparin oligosaccharides by computational analysis, Computational Biology and Chemistry, 2022, vol. 99, s.1-10, Numer artykułu:107727. DOI:10.1016/j.compbiolchem.2022.107727
  • Kogut Małgorzata, Marcisz Mateusz, Samsonov Sergey: Modeling glycosaminoglycan-protein complexes, Current Opinion in Structural Biology, 2022, vol. 73, s.1-10, Numer artykułu:102332. DOI:10.1016/j.sbi.2022.102332
  • Kuncewicz Katarzyna, Węgrzyn Katarzyna, Sieradzan Adam, Sikorska Emilia, Giedrojć Irma, Smardz Pamela, Rodziewicz-Motowidło Sylwia, Spodzieja Marta [i in.]: Targeting the HVEM protein using a fragment of glycoprotein D to inhibit formation of the BTLA/HVEM complex, Bioorganic Chemistry, 2022, vol. 122, s.1-14, Numer artykułu:105748. DOI:10.1016/j.bioorg.2022.105748
  • Lipska Agnieszka, Antoniak Anna, Wesołowski Patryk, Warszawski Alan, Samsonov Sergey, Sieradzan Andrzej: Coarse-grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins, Journal of Molecular Modeling, 2022, vol. 28, nr 7, s.1-13, Numer artykułu:201. DOI:10.1007/s00894-022-05154-3
  • Lubecka Emilia, Liwo Józef Adam: A coarse-grained approach to NMR-data-assisted modeling of protein structures, Journal of Computational Chemistry, 2022, vol. 43, nr 31, s.2047-2059. DOI:10.1002/jcc.27003
  • Marcisz Mateusz, Gaardløs Margrethe , Bojarski Krzysztof, Samsonov Sergey [i in.]: Explicit solvent repulsive scaling replica exchangemolecular dynamics (RS-REMD) in molecular modelingof protein-glycosaminoglycan complexes, Journal of Computational Chemistry, 2022, vol. 43, nr 24, s.1633-1640. DOI:10.1002/jcc.26965
  • Maszota-Zieleniak Martyna, Zsila Ferenc, Samsonov Sergey: Molecular dynamics approaches dissect molecular mechanisms underlying methylene blue - glycosaminoglycan interactions, Molecules, 2022, vol. 27, nr 9, s.1-13, Numer artykułu:2654. DOI:10.3390/molecules27092654
  • Olszewska Anna M., Sieradzan Adam, Bednarczyk Piotr [i in.]: Mitochondrial potassium channels: a novel calcitriol target, Cellular & Molecular Biology Letters, 2022, vol. 27, nr 1, s.1-20, Numer artykułu:3. DOI:10.1186/s11658-021-00299-0
  • Rojas Ana V., Maisuradze Gia, Liwo Józef Adam [i in.]: Probing protein aggregation using the coarse-grained UNRES force field, Methods in molecular biology (Clifton, N.J.), 2022, vol. 2340, s.79-104. DOI:10.1007/978-1-0716-1546-1_5
  • Roterman Irena, Sieradzan Adam, Wesołowski Patryk [i in.]: On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field, Journal of Molecular Graphics & Modelling, 2022, vol. 114, s.1-16, Numer artykułu:108166. DOI:10.1016/j.jmgm.2022.108166
  • Sage J., Bojarski Krzysztof, Samsonov Sergey [i in.]: Modulation of the expression and activity of cathepsin S in reconstructed human skin by neohesperidin dihydrochalcone, Matrix Biology, 2022, vol. 107, s.97-112. DOI:10.1016/j.matbio.2022.02.003
  • Sieradzan Adam, Czaplewski Cezary, Karczyńska Agnieszka, Lipska Agnieszka, Makowski Mariusz, Ołdziej Stanisław, Liwo Józef Adam [i in.]: Modeling the structure, dynamics, and transformations of proteins with the UNRES force field, Methods in molecular biology (Clifton, N.J.), 2022, vol. 2376, s.399-416. DOI:10.1007/978-1-0716-1716-8_23
  • Ślusarz Magdalena J.: Molecular insights into the mechanism of sugar-modified enkephalin binding to opioid receptors, Computational Biology and Chemistry, 2022, vol. 101, 107783. doi.org/10.1016/j.compbiolchem.2022.107783
  • 2021
  • Antoniak Anna, Biskupek Iga, Bojarski Krzysztof, Czaplewski Cezary, Giełdoń Artur, Kogut Mateusz, Kogut Małgorzata, Lipska Agnieszka, Liwo Józef Adam, Marcisz Mateusz, Maszota-Zieleniak Martyna, Samsonov Sergey, Sieradzan Adam, Ślusarz Magdalena, Ślusarz Rafał, Wesołowski Patryk, Zięba Karolina [i in.]: Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment, Journal of Molecular Graphics & Modelling, 2021, vol. 108, s.1-11, Numer artykułu:108008. DOI:10.1016/j.jmgm.2021.108008
  • Bertozo Luiza de Carvalho , Maszota-Zieleniak Martyna, Samsonov Sergey A. [i in.]: Binding of fluorescent dansyl amino acids in albumin: when access to the protein cavity is more important than the strength of binding, Dyes and Pigments, 2021, vol. 188, s.1-13, Numer artykułu:109195. DOI:10.1016/j.dyepig.2021.109195
  • Bojarski Krzysztof, Samsonov Sergey: Role of oligosaccharide chain polarity in protein-glycosaminoglycan interactions, Journal of Chemical Information and Modeling, 2021, vol. 61, nr 1, s.455-466. DOI:10.1021/acs.jcim.0c01402
  • Chazeirat  Thibault, Bojarski Krzysztof, Samsonov Sergey [i in.]: The abnormal accumulation of heparan sulfate in patients with mucopolysaccharidosis prevents the elastolytic activity of cathepsin V, Carbohydrate Polymers, 2021, vol. 253, s.1-15, Numer artykułu:117261. DOI:10.1016/j.carbpol.2020.117261
  • Czaplewski Cezary, Gong Zhou, Liwo Józef Adam [i in.]: Recent developments in data-assisted modeling of flexible proteins, Frontiers in Molecular Biosciences, 2021, vol. 8, s.1-8, Numer artykułu:765562. DOI:10.3389/fmolb.2021.765562
  • Gaardløs Margrethe , Samsonov Sergey A., Sletmoen Marit [i in.]: Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4, Glycobiology, 2021, vol. 31, nr 12, s.1616-1635. DOI:10.1093/glycob/cwab025
  • Gondelaud Frank, Bouakil Mathilde, Liwo Józef Adam [i in.]: Extended disorder at the cell surface: the conformational landscape of the ectodomains of syndecans, Matrix Biology Plus, 2021, vol. 12, s.1-19, Numer artykułu:100081. DOI:10.1016/j.mbplus.2021.100081
  • Grabowska Ola, Kogut Małgorzata, Żamojć Krzysztof, Samsonov Sergey, Makowska Joanna, Tesmar Aleksandra, Chmur Katarzyna, Wyrzykowski Dariusz, Chmurzyński Lech: Effect of tetraphenylborate on physicochemical properties of bovine serum albumin, Molecules, 2021, vol. 26, nr 21, s.1-17, Numer artykułu:6565. DOI:10.3390/molecules26216565
  • Karska Natalia, Graul Małgorzata, Sikorska Emilia, Ślusarz Magdalena, Kasprzykowski Franciszek, Kubiś Agnieszka, Lipińska Andrea, Rodziewicz-Motowidło Sylwia [i in.]: Investigation of the effects of primary structure modifications within the RRE motif on the conformation of synthetic bovine herpesvirus 1‐encoded UL49.5 protein fragments, Chemistry & Biodiversity, 2021, vol. 18, nr 2, s.1-16, Numer artykułu:e2000883. DOI:10.1002/cbdv.202000883
  • Kogut Małgorzata, Maszota-Zieleniak Martyna, Marcisz Mateusz, Samsonov Sergey: Computational insights into the calcium ions role in protein-glycosaminoglycan systems, Physical Chemistry Chemical Physics, 2021, vol. 23, nr 5, s.3519-3530. DOI:10.1039/D0CP05438K
  • Kogut Mateusz, Gong Zhou, Liwo Józef Adam [i in.]: Pseudopotentials for coarse‐grained cross‐link‐assisted modeling of protein structures, Journal of Computational Chemistry, 2021, vol. 42, nr 29, s.2054-2067. DOI:10.1002/jcc.26736
  • Krupa Paweł*, Spodzieja Marta, Sieradzan Adam: Prediction of CD28-CD86 protein complex structure using different level of resolution approach, Journal of Molecular Graphics & Modelling, 2021, vol. 103, s.1-8, Numer artykułu:107802. DOI:10.1016/j.jmgm.2020.107802
  • Krupa Paweł*, Karczyńska Agnieszka, Liwo Józef Adam, Czaplewski Cezary [i in.]: UNRES-Dock-protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations, Bioinformatics, 2021, vol. 37, nr 11, s.1613-1615. DOI:10.1093/bioinformatics/btaa897
  • Kryshtafovych Andriy, Czaplewski Cezary, Kogut Mateusz, Liwo Józef Adam, Lubecka Emilia [i in.]: Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment, Proteins-Structure Function and Bioinformatics, 2021, vol. 89, nr 12, s.1987-1996. DOI:10.1002/prot.26231
  • Künze Georg, Huster Daniel, Samsonov Sergey A.: Investigation of the structure of regulatory proteins interacting with glycosaminoglycans by combining NMR spectroscopy and molecular modeling - the beginning of a wonderful friendship, Biological Chemistry, 2021, vol. 402, nr 11, s.1337-1355. DOI:10.1515/hsz-2021-0119
  • Lensink Marc F., Antoniak Anna, Czaplewski Cezary, Giełdoń Artur, Kogut Mateusz, Lipska Agnieszka, Liwo Józef Adam, Maszota-Zieleniak Martyna, Sieradzan Adam, Ślusarz Rafał, Wesołowski Patryk, Zięba Karolina [i in.]: Prediction of protein assemblies, the next frontier: the CASP14‐CAPRI experiment, Proteins-Structure Function and Bioinformatics, 2021, vol. 89, nr 12, s.1800-1823. DOI:10.1002/prot.26222
  • Liwo Józef Adam, Czaplewski Cezary, Sieradzan Adam, Lipska Agnieszka, Samsonov Sergey [i in.]: Theory and practice of coarse-grained molecular dynamics of biologically important systems, Biomolecules, 2021, vol. 11, nr 9, s.1-31, Numer artykułu:1347. DOI:10.3390/biom11091347
  • Lubecka Emilia, Liwo Józef Adam: ESCASA: analytical estimation of atomic coordinates rom coarse-grained geometry for nuclear-magnetic-resonance-assisted protein structure modeling. I. Backbone and Hβ protons, Journal of Computational Chemistry, 2021, vol. 42, nr 22, s.1579-1589. DOI:10.1002/jcc.26695
  • Marcisz Mateusz, Maszota-Zieleniak Martyna, Samsonov Sergey [i in.]: Advanced molecular dynamics approaches to model a tertiary complex APRIL/TACI with long glycosaminoglycans, Biomolecules, 2021, vol. 11, nr 9, s.1-12, Numer artykułu:1349. DOI:10.3390/biom11091349
  • Marcisz Mateusz, Lipska Agnieszka G., Samsonov Sergey A. [i in.]: Further analyses of APRIL/APRIL-receptor/glycosaminoglycan interactions by biochemical assays linked to computational studies, Glycobiology, 2021, vol. 31, nr 7, s.772-786. DOI:10.1093/glycob/cwab016
  • Marcisz Mateusz, Zacharias Martin , Samsonov Sergey: Modeling protein–glycosaminoglycan complexes: does the size matter?, Journal of Chemical Information and Modeling, 2021, vol. 61, nr 9, s.4475-4485. DOI:10.1021/acs.jcim.1c00664
  • Maszota-Zieleniak Martyna, Zsila Ferenc, Samsonov Sergey: Computational insights into heparin-small molecule interactions: evaluation of the balance between stacking and non-stacking binding modes, Carbohydrate Research, 2021, vol. 507, s.1-12, Numer artykułu:108390. DOI:10.1016/j.carres.2021.108390
  • Maszota-Zieleniak Martyna, Marcisz Mateusz, Kogut Małgorzata M., Samsonov Sergey A. [i in.]: Evaluation of replica exchange with repulsive scaling approach for docking glycosaminoglycans, Journal of Computational Chemistry, 2021, vol. 42, nr 15, s.1040-1053. DOI:10.1002/jcc.26496
  • Maszota-Zieleniak Martyna, Danielsson Annemarie, Samsonov Sergey: The potential role of glycosaminoglycans in serum amyloid A fibril formation by in silico approaches, Matrix Biology Plus, 2021, vol. 12, s.1-16, Numer artykułu:100080. DOI:10.1016/j.mbplus.2021.100080
  • Mazuryk Jarosław, Puchalska Izabela, Ślusarz Magdalena, Ruczyński Jarosław, Rekowski Piotr, Skowron Piotr, Rodziewicz-Motowidło Sylwia, Mucha Piotr [i in.]: PTD4 peptide increases neural viability in an in vitro model of acute ischemic stroke, International Journal of Molecular Sciences, 2021, vol. 22, nr 11, s.1-22, Numer artykułu:6086. DOI:10.3390/ijms22116086
  • Samsonov Sergey A., Zsila Ferenc, Maszota-Zieleniak Martyna: Acute phase α1-acid glycoprotein as a siderophore-capturing component of the human plasma: a molecular modeling study, Journal of Molecular Graphics & Modelling, 2021, vol. 105, s.1-11, Numer artykułu:107861. DOI:10.1016/j.jmgm.2021.107861
  • Sieradzan Adam, Korneev Anatolii, Begun Alexander [i in.]: Investigation of phosphorylation-induced folding of an intrinsically disordered protein by coarse-grained molecular dynamics, Journal of Chemical Theory and Computation, 2021, vol. 17, nr 5, s.3203-3220. DOI:10.1021/acs.jctc.1c00155
  • Sieradzan Adam, Czaplewski Cezary, Bielicka-Giełdoń Aleksandra, Giełdoń Artur [i in.]: Theoretical investigation of the structural insights of the interactions of γ-Fe2O3 nanoparticle with (EMIM TFSI) ionic liquid, Journal of Molecular Liquids, 2021, nr 340, s.1-13, Numer artykułu:117198. DOI:10.1016/j.molliq.2021.117198
  • Tesmar Aleksandra, Kogut Małgorzata, Żamojć Krzysztof, Grabowska Ola, Chmur Katarzyna, Samsonov Sergey, Makowska Joanna, Wyrzykowski Dariusz, Chmurzyński Lech: Physicochemical nature of sodium dodecyl sulfate interactions with bovine serum albumin revealed by interdisciplinary approaches, Journal of Molecular Liquids, 2021, vol. 340, s.1-10, Numer artykułu:117185. DOI:10.1016/j.molliq.2021.117185
  • 2020
  • Bojarski Krzysztof, Karczyńska Agnieszka, Samsonov Sergey: Role of glycosaminoglycans in procathepsin B maturation: molecular mechanism elucidated by a computational study, Journal of Chemical Information and Modeling, 2020, vol. 60, nr 4, s.2247-2256. DOI:10.1021/acs.jcim.0c00023
  • Chrabąszczewska Magdalena, Sieradzan Adam, Rodziewicz-Motowidło Sylwia [i in.]: Structural characterization of covalently stabilized human cystatin C oligomers, International Journal of Molecular Sciences, 2020, vol. 21, nr 16, s.1-17, Numer artykułu:5860. DOI:10.3390/ijms21165860
  • Gitlin-Domagalska Agata, Dębowski Dawid, Gucwa Katarzyna, Starego Dominika, Ptaszyńska Natalia, Sieradzan Adam, Karczyńska Agnieszka, Samsonov Sergey, Łęgowska Anna, Rolka Krzysztof [i in.]: Truncation of Huia versabilis Bowman-Birk inhibitor increases its selectivity, matriptase-1 inhibitory activity and proteolytic stability, Biochimie, 2020, vol. 171-172, s.178-186. DOI:10.1016/j.biochi.2020.03.006
  • Glashagen Glenn, Uciechowska-Kaczmarzyk Urszula, Samsonov Sergey [i in.]: Coarse‐grained and atomic resolution biomolecular docking with the ATTRACT approach, Proteins-Structure Function and Bioinformatics, 2020, vol. 88, nr 8, s.1018-1028. DOI:10.1002/prot.25860
  • Gorbikova Elena, Samsonov Sergey, Kalendar Ruslan: Probing the proton-loading site of cytochrome c oxidase using time-resolved Fourier transform infrared spectroscopy, Molecules, 2020, vol. 25, nr 15, s.1-14, Numer artykułu:3393. DOI:10.3390/molecules25153393
  • Karczyńska Agnieszka, Zięba Karolina, Uciechowska Urszula, Lubecka Emilia, Lipska Agnieszka, Sikorska Celina, Samsonov Sergey, Sieradzan Adam, Giełdoń Artur, Liwo Adam, Ślusarz Rafał, Ślusarz Magdalena, Czaplewski Cezary [i in.]: Improved consensus-fragment selection intemplate-assisted prediction of protein structureswith the UNRES force field in CASP13, Journal of Chemical Information and Modeling, 2020, vol. 60, nr 3, s.1844-1864. DOI:10.1021/acs.jcim.9b00864
  • Kuncewicz Katarzyna, Sieradzan Adam, Karczyńska Agnieszka, Orlikowska Marta, Rodziewicz-Motowidło Sylwia, Spodzieja Marta [i in.]: Fragments of gD protein as inhibitors of BTLA/HVEM complex formation-design, synthesis, and cellular studies, International Journal of Molecular Sciences, 2020, vol. 21, nr 22, s.1-19, Numer artykułu:8876. DOI:10.3390/ijms21228876
  • Lecaille Fabien , Bojarski Krzysztof, Samsonov Sergey [i in.]: Rat cathepsin K: enzymatic specificity and regulation of its collagenolytic activity, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2020, vol. 1868, nr 2, s.1-11, Numer artykułu:140318. DOI:10.1016/j.bbapap.2019.140318
  • Liwo Józef Adam, Czaplewski Cezary: Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: application to the UNRES model of proteins, Journal of Chemical Physics, 2020, vol. 152, nr 5, s.1-15, Numer artykułu:054902. DOI:10.1063/1.5138991
  • Liwo Józef Adam, Czaplewski Cezary, Sieradzan Adam, Lubecka Emilia, Lipska Agnieszka, Golon Łukasz, Karczyńska Agnieszka, Makowski Mariusz, Ganzynkowicz Robert, Giełdoń Artur [i in.]: Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers, Progress in Molecular Biology and Translational Science, 2020, vol. 170, s.73-122. DOI:10.1016/bs.pmbts.2019.12.004
  • Sevink G. J. Agur, Liwo Józef Adam, Asinari Pietro [i in.]: Unfolding the prospects of computational (bio)materials modeling , Journal of Chemical Physics, 2020, vol. 153, nr 10, s.1-12, Numer artykułu:100901. DOI:10.1063/5.0019773
  • Spodzieja Marta, Kuncewicz Katarzyna, Sieradzan Adam, Karczyńska Agnieszka, Węgrzyn Katarzyna, Maszota-Zieleniak Martyna, Rodziewicz-Motowidło Sylwia [i in.]: Disulfide-linked peptides for blocking BTLA/HVEM binding, International Journal of Molecular Sciences, 2020, vol. 21, nr 2, s.1-18, Numer artykułu:636. DOI:10.3390/ijms21020636
  • Zięba Karolina, Czaplewski Cezary, Liwo Józef Adam [i in.]: Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models, Physical Chemistry Chemical Physics, 2020, vol. 22, nr 8, s.4758-4771. DOI:10.1039/C9CP06627F
  • Zsila Ferenc, Samsonov Sergey, Maszota-Zieleniak Martyna: Mind your dye: the amyloid sensor thioflavin T interacts with sulfated glycosaminoglycans used to induce cross-β-sheet motifs, Journal of Physical Chemistry B, 2020, vol. 124, nr 51, s.11625-11633. DOI:10.1021/acs.jpcb.0c08273
  • 2019  
  • Bojarski Krzysztof, Sieradzan Adam, Samsonov Sergey: Molecular dynamics insights into protein-glycosaminoglycan systems from microsecond-scale simulations, Biopolymers, 2019, vol. 110, nr 7, s.1-15, Numer artykułu:e23252. DOI:10.1002/bip.23252
  • Bojarski Krzysztof, Becher Jana, Samsonov Sergey [i in.]: Synthesis and in silico characterization of artificially phosphorylated glycosaminoglycans, Journal of Molecular Structure, 2019, vol. 1197, s.401-416. DOI:10.1016/j.molstruc.2019.07.064
  • Drobot Björn, Schmidt Moritz, Samsonov Sergey [i in.]: Cm3+/Eu3+ induced structural, mechanistic and functional implications for calmodulin, Physical Chemistry Chemical Physics, 2019, vol. 21, nr 38, s.21213-21222. DOI:10.1039/C9CP03750K
  • Fajardo J. Eduardo, Czaplewski Cezary, Karczyńska Agnieszka, Liwo Józef Adam, Lubecka Emilia, Sieradzan Adam, Sikorska Celina [i in.]: Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13, Proteins-Structure Function and Bioinformatics, 2019, vol. 87, nr 12, s.1283-1297. DOI:10.1002/prot.25816
  • Ilyechova Ekaterina Y., Miliukhina Irina V., Samsonov Sergey [i in.]: Case of early-onset Parkinson’s disease in a heterozygous mutation carrier of the ATP7B gene, Journal of Personalized Medicine, 2019, vol. 9, nr 3, s.1-16, Numer artykułu:41. DOI:10.3390/jpm9030041
  • Karska Natalia, Graul Małgorzata, Sikorska Emilia, Ślusarz Magdalena, Kasprzykowski Franciszek, Lipińska Andrea, Rodziewicz-Motowidło Sylwia [i in.]: Structure determination of UL49.5 transmembrane protein from bovine herpesvirus 1 by NMR spectroscopy and molecular dynamics, Biochimica et Biophysica Acta-Biomembranes, 2019, vol. 1861, nr 5, s.926-938. DOI:10.1016/j.bbamem.2019.02.005
  • Kohut Gergely, Sieradzan Adam, Liwo Józef Adam, Samsonov Sergey [i in.]: The molecular mechanism of structural changes in the antimicrobial peptide CM15 upon complex formation with drug molecule suramin: a computational analysis, Physical Chemistry Chemical Physics, 2019, vol. 21, nr 20, s.10644-10659. DOI:10.1039/C9CP00471H
  • Kuncewicz Katarzyna, Spodzieja Marta, Sieradzan Adam, Karczyńska Agnieszka, Rodziewicz-Motowidło Sylwia [i in.]: A structural model of the immune checkpoint CD160-HVEM complex derived from HDX-mass spectrometry and molecular modeling, Oncotarget, 2019, vol. 10, nr 4, s.536-550. DOI:10.18632/oncotarget.26570
  • Lensink Marc F., Karczyńska Agnieszka, Czaplewski Cezary, Lubecka Emilia, Lipska Agnieszka, Golon Łukasz, Samsonov Sergey, Liwo Józef Adam [i in.]: Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment, Proteins-Structure Function and Bioinformatics, 2019, vol. 87, nr 12, s.1200-1221. DOI:10.1002/prot.25838
  • Liwo Józef Adam, Sieradzan Adam, Lipska Agnieszka, Czaplewski Cezary, Żmudzińska Wioletta, Hałabis Anna, Ołdziej Stanisław [i in.]: A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation , Journal of Chemical Physics, 2019, vol. 150, nr 15, s.1-25, Numer artykułu:155104. DOI:10.1063/1.5093015
  • Liwo Józef Adam, Sieradzan Adam, Czaplewski Cezary: Formation of secondary and supersecondary structure of proteins as a result of coupling between local and backbone-electrostatic interactions: a view through cluster-cumulant scope, Methods in molecular biology (Clifton, N.J.), 2019, vol. 1958, s.133-146. DOI:10.1007/978-1-4939-9161-7_7
  • Liwo Józef Adam, Lubecka Emilia: Introduction of a bounded penalty function in contact‐assisted simulations of protein structures to omit false restraints, Journal of Computational Chemistry, 2019, vol. 40, nr 25, s.2164-2178. DOI:10.1002/jcc.25847
  • Lubecka Emilia, Karczyńska Agnieszka, Lipska Agnieszka, Sieradzan Adam, Zięba Karolina, Sikorska Celina, Uciechowska Urszula, Samsonov Sergey, Golon Łukasz, Giełdoń Artur, Czaplewski Cezary, Ślusarz Rafał, Ślusarz Magdalena, Liwo Józef Adam [i in.]: Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment, Journal of Molecular Graphics & Modelling, 2019, vol. 92, s.154-166. DOI:10.1016/j.jmgm.2019.07.013
  • Penk Anja, Baumann Lars, Samsonov Sergey [i in.]: NMR and molecular modeling reveal specificity of the interactions between CXCL14 and glycosaminoglycans, Glycobiology, 2019, vol. 29, nr 10, s.715-725. DOI:10.1093/glycob/cwz047
  • Plotnikova Marina A., Uciechowska-Kaczmarzyk Urszula, Samsonov Sergey [i in.]: Meglumine acridone acetate, the ionic salt of CMA and N-methylglucamine, induces apoptosis in human PBMCs via the mitochondrial pathway, Scientific Reports, 2019, vol. 9, s.1-16, Numer artykułu:18240. DOI:10.1038/s41598-019-54208-9
  • Potthoff Jan, Bojarski Krzysztof, Lipska Agnieszka, Liwo Józef Adam, Samsonov Sergey [i in.]: Analysis of procollagen C-proteinase enhancer-1/glycosaminoglycan binding sites and of the potential role of calcium ions in the interaction, International Journal of Molecular Sciences, 2019, vol. 20, nr 20, s.1-24, Numer artykułu:5021. DOI:10.3390/ijms20205021
  • Samsonov Sergey, Freza Sylwia, Zsila Ferenc: In silico analysis of heparin and chondroitin sulfate binding mechanisms of the antiprotozoal drug berenil and pentamidine, Carbohydrate Research, 2019, vol. 482, s.1-8, Numer artykułu:107742. DOI:10.1016/j.carres.2019.107742
  • Samsonov Sergey, Lubecka Emilia, Bojarski Krzysztof, Ganzynkowicz Robert, Liwo Józef Adam: Local and long range potentials for heparin-protein systems for coarse-grained simulations, Biopolymers, 2019, vol. 110, nr 8, s.1-12, Numer artykułu:e23269. DOI:10.1002/bip.23269
  • Samsonov Sergey, Zacharias Martin, Chauvot de Beauchene Isaure: Modeling large protein-glycosaminoglycan complexes using a fragment‐based approach, Journal of Computational Chemistry, 2019, vol. 40, nr 14, s.1429-1439. DOI:10.1002/jcc.25797
  • Sieradzan Adam, Bogunia  Małgorzata, Mech Paulina, Ganzynkowicz Robert, Giełdoń Artur, Liwo Józef Adam, Makowski Mariusz: Introduction of phosphorylated residues into the UNRES coarse-grained model: toward modeling of signaling processes, Journal of Physical Chemistry B, 2019, vol. 123, nr 27, s.5721-5729. DOI:10.1021/acs.jpcb.9b03799
  • Sikorska Celina: Magnesium-based oxyfluoride superatoms: design, structure, and electronic properties, Journal of Chemical Information and Modeling, 2019, vol. 59, nr 5, s.2175-2189. DOI:10.1021/acs.jcim.9b00083
  • Sikorska Celina: Magnesium‐based clusters as building blocks of electrolytes in lithium‐ion batteries, ChemPhysChem, 2019, vol. 20, nr 17, s.2236-2246. DOI:10.1002/cphc.201900318
  • Uciechowska-Kaczmarzyk Urszula, Chauvot de Beauchene Isaure, Samsonov Sergey: Docking software performance in protein-glycosaminoglycan systems, Journal of Molecular Graphics & Modelling, 2019, vol. 90, s.42-50. DOI:10.1016/j.jmgm.2019.04.001
  • Zięba Karolina, Ślusarz Magdalena, Ślusarz Rafał, Liwo Józef Adam, Czaplewski Cezary, Sieradzan Adam: Extension of the UNRES coarse-grained force field to membrane proteins in the lipid bilayer, Journal of Physical Chemistry B, 2019, vol. 123, nr 37, s.7829-7839. DOI:10.1021/acs.jpcb.9b06700
  • 2018
  • Czaplewski Cezary, Karczyńska Agnieszka, Sieradzan Adam, Liwo Józef Adam: UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics, Nucleic Acids Research, 2018, vol. 46, nr W1, s.W304-W309. DOI:10.1093/nar/gky328
  • Faraggi Eshel, Krupa Paweł, Liwo Józef Adam [i in.]: Reoptimized UNRES potential for protein model quality assessment, Genes, 2018, vol. 9, nr 12, s.1-17. DOI:10.3390/genes9120601
  • Grzeszczuk Magdalena Joanna, Giełdoń Artur, Czaplewski Cezary, Liwo Józef Adam [i in.]: Impact of selected amino acids of HP0377 (Helicobacter pylori thiol oxidoreductase) on its functioning as a CcmG (cytochrome c maturation) protein and Dsb (disulfide bond) isomerase, PLoS ONE, 2018, vol. 13, nr 4, s.1-27. DOI:10.1371/journal.pone.0195358
  • Karczyńska Agnieszka, Giełdoń Artur, Liwo Józef Adam, Czaplewski Cezary [i in.]: Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information, Proteins-Structure Function and Bioinformatics, 2018, vol. 86, s.228-239. DOI:10.1002/prot.25421
  • Karczyńska Agnieszka, Giełdoń Artur, Bojarski  Krzysztof, Zaborowski Bartłomiej, Liwo Józef Adam, Ślusarz Rafał, Ślusarz Magdalena, Czaplewski Cezary [i in.]: Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets, Journal of Molecular Graphics & Modelling, 2018, vol. 83, s.92-99. DOI:10.1016/j.jmgm.2018.05.008
  • Keasar Chen, Ganzynkowicz Robert, Giełdoń Artur, Golon Łukasz, Krupa Paweł, Lipska Agnieszka, Liwo Adam, Mozolewska Magdalena, Sieradzan Adam, Ślusarz Magdalena, Ślusarz Rafał, Wirecki Tomasz, Baranowski Maciej, Zaborowski Bartłomiej, Czaplewski Cezary, Ołdziej Stanisław [i in.]: An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12, Scientific Reports, 2018, vol. 8, s.1-18, Numer artykułu: 9939. DOI:10.1038/s41598-018-26812-8
  • Kohut Gergely, Liwo Józef Adam, Samsonov Sergey [i in.]: Protein-ligand interaction energy-based entropy calculations: fundamental challenges for flexible systems, Journal of Physical Chemistry B, 2018, vol. 122, nr 32, s.7821-7827. DOI:10.1021/acs.jpcb.8b03658
  • Krupa Paweł*, Wales David J., Sieradzan Adam: Computational studies of the mechanical stability for single-strand break DNA, Journal of Physical Chemistry B, 2018, vol. 122, nr 34, s.8166-8173. DOI:10.1021/acs.jpcb.8b05417
  • Lubecka Emilia, Sieradzan Adam, Czaplewski Cezary, Liwo Józef Adam [i in.]: High performance computing with coarse grained model of biological macromolecules, Supercomputing Frontiers and Innovations, 2018, vol. 5, nr 2, s.63-75. DOI:10.14529/jsfi180206
  • Nordsieck Karoline, Baumann Lars, Samsonov Sergey [i in.]: The effect of interleukin-8 truncations on its interactions with glycosaminoglycans, Biopolymers, 2018, vol. 109, nr 10, s.1-12, Numer artykułu:e23103. DOI:10.1002/bip.23103
  • Paszkiewicz Monika, Sikorska Celina, Stepnowski Piotr [i in.]: Helical multi-walled carbon nanotubes as an efficient material for the dispersive solid-phase extraction of low and high molecular weight polycyclic aromatic hydrocarbons from water samples: theoretical study, Water Air and Soil Pollution, 2018, vol. 229, nr 8, s.1-15, Numer artykułu:253. DOI:10.1007/s11270-018-3884-0
  • Sieradzan Adam, Giełdoń Artur, Liwo Józef Adam [i in.]: A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields, Journal of Computational Chemistry, 2018, vol. 39, nr 28, s.2360-2370. DOI:10.1002/jcc.25571
  • Sieradzan Adam, Golon Łukasz, Liwo Józef Adam: Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing, Physical Chemistry Chemical Physics, 2018, vol. 20, nr 29, s.19656-19663. DOI:10.1039/C8CP03018A
  • Sieradzan Adam, Lipska Agnieszka, Lubecka Emilia: Shielding effect in protein folding, Journal of Molecular Graphics & Modelling, 2018, vol. 79, s.118-132. DOI:10.1016/j.jmgm.2017.10.018
  • Sikorska Celina: Mg3F7: A superhalogen with potential for new nanomaterials design, International Journal of Quantum Chemistry, 2018, vol. 118, nr 21, s.1-15. DOI:10.1002/qua.25728
  • Sikorska Celina: Oxidizing metal oxides with polynuclear superhalogen: an ab initio study, Journal of Physical Chemistry A, 2018, vol. 122, nr 37, s.7328-7338. DOI:10.1021/acs.jpca.8b05095
  • Uciechowska-Kaczmarzyk Urszula, Bojarski  Krzysztof, Samsonov Sergey [i in.]: Molecular dynamics-based model of VEGF-A and its heparin interactions, Journal of Molecular Graphics & Modelling, 2018, vol. 82, s.157-166. DOI:10.1016/j.jmgm.2018.04.015
  • Vallet Sylvain D., Uciechowska-Kaczmarzyk Urszula, Liwo Józef Adam, Samsonov Sergey [i in.]: Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners, Scientific Reports, 2018, vol. 8, s.1-16, Numer artykułu:11768. DOI:10.1038/s41598-018-30190-6
  • Zsila Ferenc, Samsonov Sergey: Molecular interactions of the anticancer agent ellipticine with glycosaminoglycans by in silico analysis, Carbohydrate Research, 2018, vol. 462, s.28-33. DOI:10.1016/j.carres.2018.03.014
  • 2017  
  • Johnston Travis, Zhang Boyu, Liwo Józef Adam [i in.]: In situ data analytics and indexing of protein trajectories, Journal of Computational Chemistry, 2017, vol. 38, nr 16, s.1419-1430. DOI:10.1002/jcc.24729
  • Karczyńska Agnieszka, Czaplewski Cezary, Liwo Józef Adam [i in.]: Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian Replica Exchange coarse-grained molecular dynamics simulations of proteins, Journal of Computational Chemistry, 2017, vol. 38, nr 31, s.2730-2746. DOI:10.1002/jcc.25070
  • Krupa Paweł, Sieradzan Adam, Liwo Józef Adam [i in.]: Dynamics of disulfide-bond disruption and formation in the thermal unfolding of ribonuclease A, Journal of Chemical Theory and Computation, 2017, vol. 13, nr 11, s.5721-5730. DOI:10.1021/acs.jctc.7b00724
  • Krupa Paweł*, Hałabis Anna, Żmudzińska Wioletta, Ołdziej Stanisław, Liwo Józef Adam [i in.]: Maximum likelihood calibration of the UNRES force field for simulation of protein structure and dynamics, Journal of Chemical Information and Modeling, 2017, vol. 57, nr 9, s.2364-2377. DOI:10.1021/acs.jcim.7b00254
  • Lubecka Emilia, Liwo Józef Adam: A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O1 -> 4 -bonded polyglucose chains, Journal of Chemical Physics, 2017, vol. 147, nr 11, s.1-13, Numer artykułu:115101. DOI:10.1063/1.4994130
  • Makowski Mariusz, Liwo Józef Adam, Scheraga Harold A.: Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino acid side chains in water. VII. Charged-hydrophobic/polar and polar-hydrophobic/polar side chains, Journal of Physical Chemistry B, 2017, vol. 121, nr 2, s.379-390. DOI:10.1021/acs.jpcb.6b08541
  • Mioduszewska Katarzyna, Dołżonek Joanna, Wyrzykowski Dariusz, Sikorska Celina, Toński Michał, Kaczyński Zbigniew, Stepnowski Piotr, Białk-Bielińska Anna [i in.]: Overview of experimental and computational methods for the determination of the pKa values of 5-fluorouracil, cyclophosphamide, ifosfamide, imatinib and methotrexate, Trac-Trends in Analytical Chemistry, 2017, vol. 97, s.283-296. DOI:10.1016/j.trac.2017.09.009
  • Mozolewska Magdalena, Sieradzan Adam, Niadzvedtski  Andrei, Czaplewski Cezary, Liwo Józef Adam, Krupa Paweł: Role of the sulfur to α-carbon thioether bridges in thurincin H, Journal of Biomolecular Structure & Dynamics, 2017, vol. 35, nr 13, s.2868-2879. DOI:10.1080/07391102.2016.1234414
  • Sieradzan Adam, Makowski Mariusz, Augustynowicz Antoni, Liwo Józef Adam: A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains, Journal of Chemical Physics, 2017, vol. 146, nr 12, s.1-28, Numer artykułu:124106. DOI:10.1063/1.4978680
  • Sieradzan Adam, Jakubowski Rafał: Introduction of steered molecular dynamics into UNRES coarse-grained simulations package, Journal of Computational Chemistry, 2017, vol. 38, nr 8, s.553-562. DOI:10.1002/jcc.24685
  • Sieradzan Adam, Krupa Paweł*, Wales David J.: What makes telomeres unique?, Journal of Physical Chemistry B, 2017, vol. 121, nr 10, s.2207-2219. DOI:10.1021/acs.jpcb.6b08780
  • Urbaszek Piotr, Gajewicz Agnieszka, Sikorska Celina, Puzyn Tomasz [i in.]: Modeling adsorption of brominated, chlorinated and mixed bromo/chloro-dibenzo-p-dioxins on C60 fullerene using Nano-QSPR, Beilstein Journal of Nanotechnology, 2017, vol. 8, s.752-761. DOI:10.3762/bjnano.8.78
  • Żurawa-Janicka Dorota, Wenta Tomasz, Jarząb Mirosław, Skórko-Glonek Joanna, Glaza Przemysław, Giełdoń Artur, Ciarkowski Jerzy, Lipińska Barbara: Structural insights into the activation mechanisms of human HtrA serine proteases, Archives of Biochemistry and Biophysics, 2017, vol. 621, s.6-23. DOI:10.1016/j.abb.2017.04.004
  • 2016
  • Dai Jin, Niemi Antti J., Sieradzan Adam [i in.]: Bloch spin waves and emergent structure in protein folding with HIV envelope glycoprotein as an example, Physical Review E, 2016, vol. 93, nr 3, s.1-17. DOI:10.1103/PhysRevE.93.032409
  • Giełdoń Artur, Żurawa-Janicka Dorota, Jarząb Mirosław, Wenta Tomasz, Lipińska Barbara, Ciarkowski Jerzy [i in.]: Distinct 3D architecture and dynamics of the human HtrA2(Omi) protease and its mutated variants, Plos One, 2016, vol. 11, nr 8, s.1-19. DOI:10.1371/journal.pone.0161526
  • Jarząb Mirosław, Wenta Tomasz, Żurawa-Janicka Dorota, Giełdoń Artur, Wysocka Magdalena, Glaza Przemysław, Skórko-Glonek Joanna, Ciarkowski Jerzy, Lesner Adam, Lipińska Barbara [i in.]: Intra- and intersubunit changes accompanying thermal activation of the HtrA2(Omi) protease homotrimer, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2016, vol. 1864, nr 3, s.283-296. DOI:10.1016/j.bbapap.2015.12.002
  • Krupa Paweł, Mozolewska Magdalena, Wiśniewska Marta, Sieradzan Adam, Ganzynkowicz Robert, Lipska Agnieszka, Karczyńska Agnieszka, Ślusarz Magdalena, Ślusarz Rafał, Giełdoń Artur, Czaplewski Cezary, Jagieła Dawid, Zaborowski Bartłomiej, Liwo Józef Adam [i in.]: Performance of protein-structure predictions with the physics-based UNRES force field in CASP11, Bioinformatics, 2016, vol. 32, nr 21, s.3270-3278. DOI:10.1093/bioinformatics/btw404
  • Lipska Agnieszka, Sieradzan Adam, Giełdoń Artur, Liwo Józef Adam [i in.]: Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction, Journal of Chemical Physics, 2016, vol. 144, nr 18, s.1-11. DOI:10.1063/1.4948710
  • Lubecka Emilia, Liwo Józef Adam: New UNRES force field package with Fortran 90, Task Quarterly, 2016, vol. 20, nr 4, s.399-407. DOI:10.17466/tq2016/20.4/n
  • Lubecka Emilia, Sikorska Emilia, Sobolewski Dariusz, Prahl Adam, Ciarkowski Jerzy [i in.]: Potent antidiuretic agonists, deamino-vasopressin and desmopressin, and their inverso analogs: NMR structure and interactions with micellar and liposomic models of cell membrane, Biopolymers, 2016, vol. 106, nr 3, s.245-259. DOI:10.1002/bip.22825
  • Mozolewska Magdalena, Krupa Paweł, Zaborowski Bartłomiej, Liwo Józef Adam, Czaplewski Cezary [i in.]: Use of restraints from consensus fragments of multiple server models to enhance protein-structure prediction capability of the UNRES force field, Journal of Chemical Information and Modeling, 2016, vol. 56, nr 11, s.2263-2279. DOI:10.1021/acs.jcim.6b00189
  • Peng Xubiao, Sieradzan Adam, Niemi Antti J.: Thermal unfolding of myoglobin in the Landau-Ginzburg-Wilson approach, Physical Review E, 2016, vol. 94, nr 6, s.1-16. DOI:10.1103/PhysRevE.94.062405
  • Sikorska Celina: Are noble gas molecules able to exhibit a superhalogen nature?, RSC Advances, 2016, vol. 6, nr 105, s.103418-103427. DOI:10.1039/C6RA21933K
  • Sikorska Celina, Gajewicz Agnieszka, Urbaszek Piotr, Lubiński Łukasz, Puzyn Tomasz: Efficient way of designing fullerene derivatives based on simplified DFT calculations and QSPR modeling, Chemometrics and Intelligent Laboratory Systems, 2016, vol. 152, s.125-133. DOI:10.1016/j.chemolab.2016.02.003
  • Sikorska Celina: When a nanoparticle meets a superhalogen: a case study with C60 fullerene, Physical Chemistry Chemical Physics, 2016, vol. 18, nr 28, s.18739-18749. DOI:10.1039/C6CP00380J
  • Sikorska Emilia, Wyrzykowski Dariusz, Lubecka Emilia [i in.]: Thermodynamics, size, and dynamics of zwitterionic dodecylphosphocholine and anionic sodium dodecyl sulfate mixed micelles, Journal of Thermal Analysis and Calorimetry, 2016, vol. 123, nr 1, s.511-523. DOI:10.1007/s10973-015-4918-0
  • Wyrzykowska  Ewelina, Mikołajczyk Alicja, Sikorska Celina, Puzyn Tomasz: Development of a novel in silico model of zeta potential for metal oxide nanoparticles: a nano-QSPR approach, Nanotechnology, 2016, vol. 27, nr 44, s.1-8. DOI:10.1088/0957-4484/27/44/445702
  • 2015  
  • Gołaś  Ewa, Czaplewski Cezary, Liwo Józef Adam [i in.]: Common functionally important motions of the nucleotide-binding domain of Hsp70, Proteins-Structure Function and Bioinformatics, 2015, vol. 83, nr 2, s.282-299. DOI:10.1002/prot.24731
  • He Yi, Liwo Józef Adam, Scheraga Harold A.: Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach, Journal of Chemical Physics, 2015, vol. 143, nr 24, s.1-8. DOI:10.1063/1.4932082
  • Krupa Paweł, Mozolewska Magdalena, Czaplewski Cezary, Liwo Józef Adam [i in.]: Prediction of protein structure by template-based modeling combined with the UNRES force field, Journal of Chemical Information and Modeling, 2015, vol. 55, nr 6, s.1271-1281. DOI:10.1021/acs.jcim.5b00117
  • Lipska Agnieszka, Sieradzan Adam, Krupa Paweł, Mozolewska Magdalena, Liwo Józef Adam [i in.]: Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field, Journal of Molecular Modeling, 2015, vol. 21, nr 3, s.1-11. DOI:10.1007/s00894-015-2609-1
  • Lubecka Emilia, Sikorska Emilia, Sobolewski Dariusz, Prahl Adam, Ciarkowski Jerzy [i in.]: Arginine-, D-arginine-vasopressin, and their inverso analogues in micellar and liposomic models of cell membrane: CD, NMR, and molecular dynamics studies, European Biophysics Journal With Biophysics Letters, 2015, vol. 44, nr 8, s.727-743. DOI:10.1007/s00249-015-1071-4
  • Maisuradze Gia G., Krupa Paweł, Mozolewska Magdalena [i in.]: Preventing fibril formation of a protein by selective mutation, Proceedings of the National Academy of Sciences of the United States of America, 2015, vol. 112, nr 44, s.13549-13554. DOI:10.1073/pnas.1518298112
  • Maszota Martyna, Karska Natalia, Spodzieja Marta, Ciarkowski Jerzy, Kołodziejczyk Aleksandra, Rodziewicz-Motowidło Sylwia, Czaplewska Paulina: Structural studies of the C-terminal 19-peptide of serum amyloid A and its Pro->Ala variants interacting with human cystatin C, Journal of Molecular Recognition, 2015, vol. 28, nr 7, s.413-426. DOI:10.1002/jmr.2457
  • Mozolewska Magdalena, Krupa Paweł, Liwo Józef Adam [i in.]: Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches, Proteins-Structure Function and Bioinformatics, 2015, vol. 83, nr 8, s.1414-1426. DOI:10.1002/prot.24824
  • Rak Janusz, Chomicz Lidia, Wiczk  Justyna, Westphal  Kinga, Zdrowowicz Magdalena, Wityk Paweł, Żyndul Michał, Makurat Samanta, Golon Łukasz: Mechanisms of damage to DNA labeled with electrophilic nucleobases induced by ionizing or UV radiation, Journal of Physical Chemistry B, 2015, vol. 119, nr 26, s.8227-8238. DOI:10.1021/acs.jpcb.5b03948
  • Sieradzan Adam: Introduction of periodic boundary conditions into UNRES force field, Journal of Computational Chemistry, 2015, vol. 36, nr 12, s.940-946. DOI:10.1002/jcc.23864
  • Sieradzan Adam, Krupa Paweł, Liwo Józef Adam, Czaplewski Cezary [i in.]: Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the United Residue (UNRES) force field for protein simulations, Journal of Chemical Theory and Computation, 2015, vol. 11, nr 2, s.817-831. DOI:10.1021/ct500736a
  • Sikorska Celina, Puzyn Tomasz: The performance of selected semi-empirical and DFT methods in studying C60 fullerene derivatives, Nanotechnology, 2015, vol. 26, nr 45, s.1-10. DOI:10.1088/0957-4484/26/45/455702
  • Sikorska Celina: Toward predicting vertical detachment energies for superhalogenanions exclusively from 2-D structures, Chemical Physics Letters, 2015, vol. 625, s.157-163. DOI:10.1016/j.cplett.2015.03.002
  • Sikorska Celina: Utilizing fluoroxyl groups as ligands in superhalogen anions: an ab initio study of the M(OF)-k+1 systems (M = Li, Na, K, Be, Mg, Ca, B, Al), Chemical Physics Letters, 2015, vol. 638, s.179-186. DOI:10.1016/j.cplett.2015.08.043
  • Ślusarz Magdalena: Vasopressin V1a and V1b receptor modulators: a patent review (2012-2014), Expert Opinion on Therapeutic Patents, 2015, vol. 25, nr 6, s.711-722. DOI:10.1517/13543776.2015.1026257
  • Wiśniewska Marta, Sobolewski Emil, Ołdziej Stanisław, Liwo Józef Adam, Makowski Mariusz [i in.]: Theoretical studies of interactions between O-phosphorylated and standard amino-acid side-chain models in water, Journal of Physical Chemistry B, 2015, vol. 119, nr 27, s.8526-8534. DOI:10.1021/acs.jpcb.5b04782
  • Yin Yanping, Sieradzan Adam, Liwo Józef Adam [i in.]: Physics-based potentials for coarse-grained modeling of protein- DNA interactions, Journal of Chemical Theory and Computation, 2015, vol. 11, nr 4, s.1792-1808. DOI:10.1021/ct5009558
  • Zaborowski Bartłomiej, Jagieła Dawid, Czaplewski Cezary, Hałabis Anna, Lewandowska Agnieszka, Żmudzińska Wioletta, Ołdziej Stanisław, Karczyńska Agnieszka, Wirecki Tomasz, Liwo Józef Adam [i in.]: A maximum-likelihood approach to force-field calibration, Journal of Chemical Information and Modeling, 2015, vol. 55, nr 9, s.2050-2070. DOI:10.1021/acs.jcim.5b00395
  • 2014
  • Chomicz Lidia, Golon Łukasz, Rak Janusz: The radiosensitivity of 5- and 6-bromocytidine derivatives: electron induced DNA degradation, Physical Chemistry Chemical Physics, 2014, vol. 16, nr 36, s.19424-19428. DOI:10.1039/c4cp03139c
  • Contreras-Romo M. Citlalli, Correa-Basurto José, Ślusarz Magdalena [i in.]: Theoretical studies, synthesis, and biological activity of 1-[(4-methylphenyl)sulfonyl]-5-oxo-2,3,4,5-tetrahydro-1H-1-benzazepine-4-carbonitrile (C9) as a non-peptide antagonist of the arginine vasopressin V1a and V2 receptors, Medicinal Chemistry Research, 2014, vol. 23, nr 3, s.1581-1590. DOI:10.1007/s00044-013-0739-5
  • Contreras-Romo Martha C., Martínez-Archundia Marlet, Ślusarz Magdalena [i in.]: Exploring the ligand recognition properties of the human vasopressin V1a receptor using QSAR and molecular modeling studies, Chemical Biology & Drug Design, 2014, vol. 83, nr 2, s.207-223. DOI:10.1111/cbdd.12229
  • Figaj Donata, Giełdoń Artur, Sobiecka-Szkatuła  Anna , Koper Tomasz, Denkiewicz Milena, Banecki Bogdan, Lesner Adam, Ciarkowski Jerzy, Lipińska Barbara, Skórko-Glonek Joanna [i in.]: The LA loop as an important regulatory element of the HtrA (DegP) protease from Escherichia coli: structural and functional studies, Journal of Biological Chemistry, 2014, vol. 289, nr 22, s.15880-15893. DOI:10.1074/jbc.M113.532895
  • Golon Łukasz, Chomicz Lidia, Rak Janusz: Electron-induced single strand break in the nucleotide of 5- and 6-bromouridine: a DFT study, Chemical Physics Letters, 2014, vol. 612, s.289-294. DOI:10.1016/j.cplett.2014.08.049
  • Gołaś  Ewa, Czaplewski Cezary: Rapid communication: Computational simulation and analysis of a candidate for the design of a novel silk-based biopolymer, Biopolymers, 2014, vol. 101, nr 9, s.915-923. DOI:10.1002/bip.22494
  • Kachlishvili Khatuna, Maisuradze Gia G., Liwo Józef Adam [i in.]: Accounting for a mirror-image conformation as a subtle effect in protein folding, Proceedings of the National Academy of Sciences of the United States of America, 2014, vol. 111, nr 23, s.8458-8463. DOI:10.1073/pnas.1407837111
  • Karczyńska Agnieszka, Zaborowski Bartłomiej, Ślusarz Magdalena: Investigation of interactions between dermorphin analogs and μ-opioid receptor, Task Quarterly, 2014, vol. 18, nr 4, s.331-336
  • Khoury George A., Liwo Józef Adam, Krupa Paweł, Mozolewska Magdalena, Sieradzan Adam, Wirecki Tomasz [i in.]: WeFold: a coopetition for protein structure prediction, Proteins-Structure Function and Bioinformatics, 2014, vol. 82, nr 9, s.1850-1868. DOI:10.1002/prot.24538
  • Krokhotin Andrey, Liwo Józef Adam, Maisuradze Gia G. [i in.]: Kinks, loops, and protein folding, with protein A as an example, Journal of Chemical Physics, 2014, vol. 140, nr 2, s.1-17. DOI:10.1063/1.4855735
  • Krupa Paweł, Mozolewska Magdalena, Czaplewski Cezary [i in.]: Towards mechanisms of nanotoxicity - interaction of gold nanoparticles with proteins and DNA, Task Quarterly, 2014, vol. 18, nr 4, s.337-341
  • Lesner Adam, Karna Natalia, Łęgowska Anna, Wysocka Magdalena, Guzow Katarzyna, Sieradzan Adam, Kosikowska Paulina, Łukajtis Rafał, Łęgowska Monika, Dębowski Dawid, Wiczk Wiesław, Rolka Krzysztof [i in.]: Fluorescent analogs of trypsin inhibitor SFTI-1 isolated from sunflower seeds - synthesis and applications, Biopolymers, 2014, vol. 102, nr 1, s.124-135. DOI:10.1002/bip.22442
  • Liwo Józef Adam, Baranowski Maciej, Czaplewski Cezary, Gołaś  Ewa, Jagieła Dawid, Krupa Paweł, Makowski Mariusz, Mozolewska Magdalena, Niadzvedtski  Andrei, Ołdziej Stanisław, Sieradzan Adam, Ślusarz Rafał, Wirecki Tomasz, Zaborowski Bartłomiej [i in.]: A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions, Journal of Molecular Modeling, 2014, vol. 20, nr 8, s.1-15. DOI:10.1007/s00894-014-2306-5
  • Lubecka Emilia, Sikorska Emilia: Analogi hormonów neuroprzysadkowych, Dokonania Młodych Naukowców, 2014, nr 5, cz. 1, s.40-45
  • Lubecka Emilia, Sikorska Emilia, Ciarkowski Jerzy [i in.]: Conformational studies of neurohypophyseal hormones analogues with glycoconjugates by NMR spectroscopy, Journal of Peptide Science, 2014, vol. 20, nr 6, s.406-414. DOI:10.1002/psc.2628
  • Lubecka Emilia, Sikorska Emilia: Techniki magnetycznego rezonansu jądrowego w analizie konformacyjnej peptydów i białek, Dokonania Młodych Naukowców, 2014, nr 5, cz. 1, s.34-39
  • Maciejczyk Maciej, Spasic Aleksandar, Liwo Józef Adam [i in.]: DNA duplex formation with a coarse-grained model, Journal of Chemical Theory and Computation, 2014, vol. 10, nr 11, s.5020-5035. DOI:10.1021/ct4006689
  • Mozolewska Magdalena, Krupa Paweł, Liwo Józef Adam [i in.]: Preliminary studies of interaction between nanotubes and toll-like receptors, Task Quarterly, 2014, vol. 18, nr 4, s.351-355
  • Sieradzan Adam, Niemi Antti, Peng Xubiao: Peierls-Nabarro barrier and protein loop propagation, Physical Review E, 2014, vol. 90, nr 6, s.1-9. DOI:10.1103/PhysRevE.90.062717
  • Sieradzan Adam, Niadzvedtski  Andrei, Liwo Józef Adam [i in.]: Revised backbone-virtual-bond-angle potentials to treat the L- and D-amino acid residues in the coarse-grained united residue (UNRES) force field, Journal of Chemical Theory and Computation, 2014, vol. 10, nr 5, s.2194-2203. DOI:10.1021/ct500119r
  • Yasar Fatih, Sieradzan Adam, Hansmann Ulrich H. E.: Folding and self-assembly of a small heterotetramer, Journal of Chemical Physics, 2014, vol. 140, nr 10, s.1-8. DOI:10.1063/1.4868140
  • Zhou Rui, Czaplewski Cezary, Liwo Józef Adam [i in.]: Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements, Proceedings of the National Academy of Sciences of the United States of America, 2014, vol. 111, nr 51, s.18243-18248. DOI:10.1073/pnas.1420914111
  • 2013  
  • He Y., Mozolewska Magdalena, Krupa Paweł, Sieradzan Adam, Wirecki Tomasz, Liwo Józef Adam, Jagieła Dawid, Ślusarz Rafał, Czaplewski Cezary, Ołdziej Stanisław [i in.]: Lessons from application of the UNRES force field to predictions of structures of CASP10 targets, Proceedings of the National Academy of Sciences of the United States of America, 2013, vol. 110, nr 37, s.14936-14941. DOI:10.1073/pnas.1313316110
  • He Yi, Ołdziej Stanisław, Liwo Józef Adam [i in.]: Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix, Physical Review Letters, 2013, vol. 110, nr 9, s.1-5. DOI:10.1103/PhysRevLett.110.098101
  • Krupa Paweł, Sieradzan Adam, Baranowski Maciej, Ołdziej Stanisław, Liwo Józef Adam, Czaplewski Cezary [i in.]: Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states, Journal of Chemical Theory and Computation, 2013, vol. 9, nr 10, s.4620-4632. DOI:10.1021/ct4004977
  • Lipińska Natalia, Ziętkiewicz Szymon, Sobczak Alicja, Jurczyk Agnieszka, Potocki Wojciech, Morawiec Ewa, Wawrzycka Aleksandra, Gumowski Krzysztof, Ślusarz Magdalena, Rodziewicz-Motowidło Sylwia, Chruściel Elżbieta, Liberek Krzysztof: Disruption of Ionic Interactions between the Nucleotide Binding Domain 1 (NBD1) and Middle (M) Domain in Hsp100 Disaggregase Unleashes Toxic Hyperactivity and Partial Independence from Hsp70, Journal of Biological Chemistry, 2013, vol. 288, nr 4, s.2857-2869. DOI:10.1074/jbc.M112.387589
  • Liwo Józef Adam: Coarse graining: a tool for large-scale simulations or more?, Physica Scripta, 2013, vol. 87, nr 5, s.1-4. DOI:10.1088/0031-8949/87/05/058502
  • Maisuradze Gia G., Liwo Józef Adam, Senet Patrick [i in.]: Local vs Global Motions in Protein Folding, Journal of Chemical Theory and Computation, 2013, vol. 9, nr 7, s.2907-2921. DOI:10.1021/ct4001558
  • Ślusarz Magdalena, Sikorska Emilia, Ślusarz Rafał: Interactions of vasopressin and oxytocin receptors with vasopressin analogues substituted in position 2 with 3,3′-diphenylalanine - a molecular docking study, Journal of Peptide Science, 2013, vol. 19, nr 2, s.118-126. DOI:10.1002/psc.2485
  • Żurawa-Janicka Dorota, Jarząb Mirosław, Skórko-Glonek Joanna, Lesner Adam, Gitlin-Domagalska Agata, Giełdoń Artur, Ciarkowski Jerzy, Glaza Przemysław, Lipińska Barbara [i in.]: Temperature-induced changes of HtrA2(Omi) protease activity and structure, Cell Stress & Chaperones, 2013, vol. 18, nr 1, s.35-51. DOI:10.1007/s12192-012-0355-1
  • 2012  
  • Ciarkowski Jerzy, Łuczak Sylwia, Jagieła Dawid, Sikorska Emilia [i in.]: Ensemble fits of restrained peptides' conformational equilibria to NMR data. Dependence on force fields: AMBER/8 ff03 versus ECEPP/3, Journal of Molecular Graphics & Modelling, 2012, vol. 32, s.67-74. DOI:10.1016/j.jmgm.2011.10.004
  • Dziadziuszko Halina, Kumirska Jolanta, Czerwicka Małgorzata, Lubecka Emilia, Stepnowski Piotr [i in.]: Immunochemical studies of Salmonella Dakar and Salmonella Telaviv O-antigens (serogroup O:28), FEMS Microbiology Letters, 2012, vol. 326, nr 1, s.55-61. DOI:10.1111/j.1574-6968.2011.02431.x
  • Gołaś  Ewa, Ołdziej Stanisław, Czaplewski Cezary, Liwo Józef Adam [i in.]: Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics, Journal of Chemical Theory and Computation, 2012, vol. 8, nr 5, s.1750-1764. DOI:10.1021/ct200680g
  • Hałabis Anna, Żmudzińska Wioletta, Liwo Józef Adam, Ołdziej Stanisław: Conformational dynamics of the Trp-cage miniprotein at its folding temperature, Journal of Physical Chemistry B, 2012, vol. 116, nr 23, s.6898-6907. DOI:10.1021/jp212630y
  • Krokhotin Andrey, Liwo Józef Adam, Niemi Antti J. [i in.]: Coexistence of phases in a protein heterodimer, Journal of Chemical Physics, 2012, vol. 137, nr 3, s.1-13, Numer artykułu:035101. DOI:10.1063/1.4734019
  • Lapidus Dmitrijs, Czaplewski Cezary, Liwo Józef Adam [i in.]: Multiple β-sheet molecular dynamics of amyloid formation from two ABI-SH3 domain peptides, Biopolymers, 2012, vol. 98, nr 6, s.557-566. DOI:10.1002/bip.22161
  • Lubecka Emilia, Ciarkowski Jerzy, Prahl Adam, Sikorska Emilia: Highly potent antidiuretic antagonists: conformational studies of vasopressin analogues modified with 1-naphthylalanine enantiomers at position 2, Chemical Biology & Drug Design, 2012, vol. 79, nr 6, s.1033-1042. DOI:10.1111/j.1747-0285.2012.01358.x
  • Maisuradze Gia G., Zhou Rui, Liwo Józef Adam [i in.]: Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain, Journal of Molecular Biology, 2012, vol. 420, nr 4-5, s.350-365. DOI:10.1016/j.jmb.2012.04.027
  • Makowska Joanna, Liwo Józef Adam, Chmurzyński Lech [i in.]: Influence of the length of the alanine spacer on the acidic-basic properties of the Ac-Lys-(Ala)n-Lys-NH2 peptides (n = 0, 1, 2, ..., 5), Journal of Solution Chemistry, 2012, vol. 41, nr 10, s.1738-1746. DOI:10.1007/s10953-012-9903-7
  • Makowska Joanna, Liwo Józef Adam, Żmudzińska Wioletta, Lewandowska Agnieszka, Chmurzyński Lech [i in.]: Like-charged residues at the ends of oligoalanine sequences might induce a chain reversal, Biopolymers, 2012, vol. 97, nr 4, s.240-249. DOI:10.1002/bip.22013
  • Sieradzan Adam, Scheraga Harold A. , Liwo Józef Adam: Determination of effective potentials for the stretching of Cα...Cα virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine, Journal of Chemical Theory and Computation, 2012, vol. 8, nr 4, s.1334-1343. DOI:10.1021/ct2008439
  • Sieradzan Adam, Hansman Ulrich, Liwo Józef Adam [i in.]: Extension of UNRES force field to treat polypeptide chains with D-amino acid residues, Journal of Chemical Theory and Computation, 2012, vol. 8, nr 11, s.4746-4757. DOI:10.1021/ct3005563
  • Sieradzan Adam, Liwo Józef Adam, Hansman Ulrich: Folding and self-assembly of a small protein complex, Journal of Chemical Theory and Computation, 2012, vol. 8, nr 9, s.3416-3422. DOI:10.1021/ct300528r
  • Sikorska Celina, Skurski Piotr: The saturation of the excess electron binding energy in AlnF-3n+1 (n = 1-5) anions, Chemical Physics Letters, 2012, vol. 536, s.34-38. DOI:10.1016/j.cplett.2012.03.089
  • Sikorska Celina, Skurski Piotr: Towards an understanding of the nature of superhalogen anions: an ab initio study of the Al(C6F5)-4 system, Molecular Physics, 2012, vol. 110, nr 13, s.1447-1452. DOI:10.1080/00268976.2012.656722
  • Sobolewski Emil, Ołdziej Stanisław, Wiśniewska Marta, Liwo Józef Adam, Makowski Mariusz: Toward temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. II. Molecular dynamics study of pairs of different types of interactions in water at various temperatures, Journal of Physical Chemistry B, 2012, vol. 116, nr 23, s.6844-6853. DOI:10.1021/jp212593h
  • Yin Yanping, Maisuradze Gia, Liwo Józef Adam [i in.]: Hidden protein folding pathways in free-energy landscapes uncovered by network analysis, Journal of Chemical Theory and Computation, 2012, vol. 8, nr 4, s.1176-1189. DOI:10.1021/ct200806n
  • 2011
  • He Yi, Liwo Józef Adam, Weinstein Harel [i in.]: PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics., Journal of Molecular Biology, 2011, vol. 405, nr 1, s.298-314. DOI:10.1016/j.jmb.2010.10.051
  • Kamysz Elżbieta, Mickiewicz Beata, Rodziewicz-Motowidło Sylwia, Ciarkowski Jerzy [i in.]: Synthesis, biological activity and solution structure of new analogues of the antimicrobial Gramicidin S, Journal of Peptide Science, 2011, vol. 17, nr 3, s.211-217. DOI:10.1002/psc.1314
  • Kumirska Jolanta, Czerwicka Małgorzata, Lubecka Emilia, Siedlecka Ewa Maria, Stepnowski Piotr [i in.]: Heterogeneous structure of O-antigenic part of lipopolysaccharide of Salmonella telaviv (Serogroup O:28) containing 3-acetamido-3,6-dideoxy-D-glucopyranose, Biochemistry-Moscow+, 2011, vol. 76, nr 7, s.780-790. DOI:10.1134/S000629791107008X
  • Liwo Józef Adam, He Yi, Scheraga Harold A. : Coarse-grained force field: general folding theory, Physical Chemistry Chemical Physics, 2011, vol. 13, nr 38, s.16890-16901. DOI:10.1039/c1cp20752k
  • Makowski Mariusz, Liwo Józef Adam, Sobolewski Emil [i in.]: Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains, Journal of Physical Chemistry B, 2011, vol. 115, nr 19, s.6119-6129. DOI:10.1021/jp111258p
  • Makowski Mariusz, Liwo Józef Adam, Scheraga Harold A.: Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains, Journal of Physical Chemistry B, 2011, vol. 115, nr 19, s.6130-6137. DOI:10.1021/jp111259e
  • Rojas Ana V., Liwo Józef Adam, Scheraga Harold A. : A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ1-28), Journal of Physical Chemistry B, 2011, vol. 115, nr 44, s.12978-12983. DOI:10.1021/jp2050993
  • Sikorska Celina, Skurski Piotr: Moderately reactive molecules forming stable ionic compounds with superhalogens, Inorganic Chemistry, 2011, vol. 50, nr 13, s.6384-6391. DOI:10.1021/ic200945e
  • Sikorska Celina, Ignatowska Dorota, Freza Sylwia, Skurski Piotr: The performance of selected ab initio methods in estimating electron binding energies of superhalogen anions, Journal of Theoretical & Computational Chemistry, 2011, vol. 10, nr 1, s.93-109. DOI:10.1142/S0219633611006293
  • Sikorska Celina, Freza Sylwia, Skurski Piotr, Anusiewicz Iwona: Theoretical search for alternative nine-electron ligands suitable for superhalogen anions, Journal of Physical Chemistry A, 2011, vol. 115, nr 10, s.2077-2085. DOI:10.1021/jp2000392
  • Ślusarz Magdalena: Molecular modeling study of the opioid receptor interactions with series of cyclic deltorphin analogues, Journal of Peptide Science, 2011, vol. 17, nr 8, s.554-564. DOI:10.1002/psc.1371
  • Ślusarz Rafał, Ślusarz Magdalena, Samaszko Justyna, Madaj Janusz: Conformational changes of peptidoglycan fragments during their interactions with vancomycin, Central European Journal of Chemistry, 2011, vol. 9, nr 3, s.422-431. DOI:10.2478/s11532-011-0015-9
  • 2010
  • Anusiewicz Iwona, Freza Sylwia, Sikorska Celina, Skurski Piotr: A strongly bound OF3- anion and its unstable parent neutral OF3 species, Chemical Physics Letters, 2010, vol. 493, nr 4-6, s.234-237. DOI:10.1016/j.cplett.2010.05.058
  • Danalache Bogdan A., Gutkowska Jolanta, Ślusarz Magdalena [i in.]: Oxytocin-Gly-Lys-Arg : a novel cardiomyogenic peptide, Plos One, 2010, vol. 5, nr 10, s.e13643. DOI:10.1371/journal.pone.0013643
  • Kozak Maciej, Lewandowska Agnieszka, Ołdziej Stanisław, Rodziewicz-Motowidło Sylwia, Liwo Józef Adam [i in.]: Combination of SAXS and NMR techniques as a tool for the determination of peptide structure in solution, Journal of Physical Chemistry Letters, 2010, vol. 1, nr 20, s.3128-3131. DOI:10.1021/jz101178t
  • Kozłowska Urszula, Liwo Józef Adam, Scheraga Harold A.: Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding I: the method, Journal of Computational Chemistry, 2010, vol. 31, nr 6, s.1143-1153. DOI:10.1002/jcc.21399
  • Kozłowska Urszula, Maisuradze Gia G., Liwo Józef Adam [i in.]: Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding II: results, comparison with statistical potentials, and implementation in the UNRES force field, Journal of Computational Chemistry, 2010, vol. 31, nr 6, s.1154-1167. DOI:10.1002/jcc.21402
  • Lewandowska Agnieszka, Ołdziej Stanisław, Liwo Józef Adam [i in.]: Mechanism of formation of the C-terminal β-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. III. Dynamics of long-range hydrophobic interactions, Proteins-Structure Function and Bioinformatics, 2010, vol. 78, nr 3, s.723-737. DOI:10.1002/prot.22605
  • Lewandowska Agnieszka, Ołdziej Stanisław, Liwo Józef Adam [i in.]: Mechanism of formation of the C-terminal β-hairpin of the B3 domain of the immunoglobulin-binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein, Biopolymers, 2010, vol. 93, nr 5, s.469-480. DOI:10.1002/bip.21365
  • Lewandowska Agnieszka, Ołdziej Stanisław, Liwo Józef Adam [i in.]: β-hairpin-forming peptides; models of early stages of protein folding, Biophysical Chemistry, 2010, vol. 151, nr 1-2, s.1-9. DOI:10.1016/j.bpc.2010.05.001
  • Liwo Józef Adam, Ołdziej Stanisław, Czaplewski Cezary [i in.]: Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems : toward millisecond-scale simulations of protein structure, dynamics, and thermodynamics, Journal of Chemical Theory and Computation, 2010, vol. 6, nr 3, s.890-909. DOI:10.1021/ct9004068
  • Lubecka Emilia, Kwiatkowska Anna, Ciarkowski Jerzy, Sikorska Emilia: NMR studies of new arginine vasopressin analogs modified with α-2-indanylglycine enantiomers at position 2 bound to sodium dodecyl sulfate micelles., Biophysical Chemistry, 2010, vol. 151, nr 3, s.139-148. DOI:10.1016/j.bpc.2010.06.002
  • Łęgowska Anna, Lesner Adam, Bulak Elżbieta, Jaśkiewicz Anna, Sieradzan Adam, Rolka Krzysztof [i in.]: Inhibitory activity of double-sequence analogues of trypsin inhibitor SFTI-1 from sunflower seeds: an example of peptide splicing, FEBS Journal, 2010, vol. 277, nr 10, s.2351-2359. DOI:10.1111/j.1742-4658.2010.07650.x
  • Maciejczyk Maciej, Spasic Aleksandar, Liwo Józef Adam [i in.]: Coarse-grained model of nucleic acid bases, Journal of Computational Chemistry, 2010, vol. 31, nr 8, s.1644-1655. DOI:10.1002/jcc.21448
  • Maisuradze Gia, Liwo Józef Adam, Scheraga Harold A. : Relation between free energy landscapes of proteins and dynamics, Journal of Chemical Theory and Computation, 2010, vol. 6, nr 2, s.583-595. DOI:10.1021/ct9005745
  • Maisuradze Gia G., Liwo Józef Adam, Ołdziej Stanisław [i in.]: Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein, Journal of the American Chemical Society, 2010, vol. 132, nr 27, s.9444-9452. DOI:10.1021/ja1031503
  • Maisuradze Gia G., Czaplewski Cezary, Liwo Józef Adam [i in.]: Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field, Journal of Physical Chemistry A, 2010, vol. 114, nr 13, s.4471-4485. DOI:10.1021/jp9117776
  • Makowski Mariusz, Czaplewski Cezary, Liwo Józef Adam [i in.]: Potential of mean force of association of large hydrophobic particles: toward the nanoscale limit, Journal of Physical Chemistry B, 2010, vol. 114, nr 2, s.993-1003. DOI:10.1021/jp907794h
  • Rojas Ana V., Liwo Józef Adam, Browne Dana [i in.]: Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained United-Residue force field, Journal of Molecular Biology, 2010, vol. 404, nr 3, s.537-552. DOI:10.1016/j.jmb.2010.09.057
  • Sikorska Celina, Skurski Piotr: The IP vs. VDE competition as a key factor determining the stability of the MgBX5 (X = F, Cl) compounds, Chemical Physics Letters, 2010, vol. 500, nr 4-6, s.211-216. DOI:10.1016/j.cplett.2010.10.013
  • Sikorska Celina, Freza Sylwia, Skurski Piotr: The reason why HAlCl4 acid does not exist, Journal of Physical Chemistry A, 2010, vol. 114, nr 5, s.2235-2239. DOI:10.1021/jp910589m
  • Sikorska Emilia, Kwiatkowska Anna, Sobolewski Dariusz, Ślusarz Rafał, Ślusarz Magdalena: Influence of bulky 3,3'-diphenylalanine enantiomers replacing position 2 of AVP analogues on their conformations : NMR and molecular modeling studies, European Journal of Medicinal Chemistry, 2010, vol. 45, nr 9, s.4065-4073. DOI:10.1016/j.ejmech.2010.05.066
  • Sobiecka-Szkatuła  Anna , Giełdoń Artur, Figaj Donata, Koper Tomasz, Ciarkowski Jerzy, Lipińska Barbara, Skórko-Glonek Joanna [i in.]: The role of the L2 loop in the regulation and maintaining the proteolytic activity of HtrA (DegP) protein from Escherichia coli., Archives of Biochemistry and Biophysics, 2010, vol. 500, nr 2, s.123-130. DOI:10.1016/j.abb.2010.05.028
  • Ziętkiewicz Szymon, Ślusarz Magdalena, Ślusarz Rafał, Liberek Krzysztof, Rodziewicz-Motowidło Sylwia: Conformational stability of the full-atom hexameric model of the ClpB chaperone from Escherichia coli, Biopolymers, 2010, vol. 93, nr 1, s.47-60. DOI:10.1002/bip.21294
  • Publikacja popularnonaukowa/fachowa
  • Makowski Mariusz, Liwo Józef Adam, Scheraga Harold: Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino-acid side chains in water. 1. Approximate expression for the free energy of hydrophobic association based on a Gaussian-overlap model : [erratum : Journal of Physical Chemistry B, 2007, vol. 111, iss. 11, s. 2910-2916], Journal of Physical Chemistry B, 2010, vol. 114, nr 2, s.1226. DOI:10.1021/jp911634j
  • 2009  
  • Czaplewski Cezary, Kalinowski Sebastian, Liwo Józef Adam [i in.]: Application of multiplexed replica exchange molecular dynamics to the UNRES force field: tests with α and α + β proteins, Journal of Chemical Theory and Computation, 2009, vol. 5, nr 3, s.627-640. DOI:10.1021/ct800397z
  • He Yi, Xiao Yi, Liwo Józef Adam [i in.]: Exploring the Parameter Space of the Coarse-Grained UNRES Force Field by Random Search: Selecting a Transferable Medium-Resolution Force Field, Journal of Computational Chemistry, 2009, vol. 30, nr 13, s.2127-2135. DOI:10.1002/jcc.21215
  • Maisuradze Gia, Liwo Józef Adam, Scheraga Harold A. : How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?, Physical Review Letters, 2009, vol. 102, nr 23, s.1-4, Numer artykułu:238102. DOI:10.1103/PhysRevLett.102.238102
  • Maisuradze Gia, Liwo Józef Adam, Scheraga Harold A. : Principal component analysis for protein folding dynamics, Journal of Molecular Biology, 2009, vol. 385, nr 1, s.312-329. DOI:10.1016/j.jmb.2008.10.018
  • Rodziewicz-Motowidło Sylwia, Iwaszkiewicz Justyna, Sosnowska Renata, Czaplewska Paulina, Sobolewski Emil, Szymańska Aneta, Stachowiak Krystyna, Liwo Józef Adam: The role of the Val57 amino-acid residue in the hinge loop of the human cystatin C. Conformational studies of the β2-L1-β3 segments of sild-type human cystatin C and its mutants, Biopolymers, 2009, vol. 91, nr 5, s.273-383. DOI:10.1002/bip.21140
  • Shen Hujun, Liwo Józef Adam, Scheraga Harold A. : An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics, Journal of Physical Chemistry B, 2009, vol. 113, nr 25, s.8738-8744. DOI:10.1021/jp901788q
  • Sikorska Celina, Skurski Piotr: Cationic and anionic daughters of AlOH and GaOH. An ab initio study, Chemical Physics Letters, 2009, vol. 477, nr 4-6, s.259-265. DOI:10.1016/j.cplett.2009.07.008
  • Skwierawska Agnieszka, Ołdziej Stanisław, Liwo Józef Adam [i in.]: Conformational studies of the C-terminal 16-amino-acid-residue fragment of the B3 domain of the immunoglobulin binding protein G from streptococcus, Biopolymers, 2009, vol. 91, nr 1, s.37-51. DOI:10.1002/bip.21080
  • Skwierawska Agnieszka, Makowska Joanna, Ołdziej Stanisław, Liwo Józef Adam [i in.]: Mechanism of formation of the C-terminal β-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus : I. Importance of hydrophobic interactions in stabilization of β-hairpin structure, Proteins-Structure Function and Bioinformatics, 2009, vol. 75, nr 4, s.931-953. DOI:10.1002/prot.22304
  • Skwierawska Agnieszka, Żmudzińska Wioletta, Ołdziej Stanisław, Liwo Józef Adam [i in.]: Mechanism of formation of the C-terminal β-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus : II. Interplay of local backbone conformational dynamics and long-range hydrophobic interactions in hairpin formation, Proteins-Structure Function and Bioinformatics, 2009, vol. 76, nr 3, s.637-654. DOI:10.1002/prot.22377
  • Sobiecka-Szkatuła  Anna , Giełdoń Artur, Ciarkowski Jerzy, Żurawa-Janicka Dorota, Skórko-Glonek Joanna, Lipińska Barbara [i in.]: Temperature-induced conformational changes within the regulatory loops L1-L2-LA of the HtrA heat-shock protease from Escherichia coli, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2009, vol. 1794, nr 11, s.1573-1582. DOI:10.1016/j.bbapap.2009.07.002
  • Sobolewski Emil, Makowski Mariusz, Ołdziej Stanisław, Czaplewski Cezary, Liwo Józef Adam [i in.]: Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures, Protein Engineering Design & Selection, 2009, vol. 22, nr 9, s.547-552. DOI:10.1093/protein/gzp028
  • Ślusarz Magdalena, Ślusarz Rafał: An Influence of the Aromatic Side Chains Conformations in Positions 2 and 3 of Vasopressin Analogs on Interactions with Vasopressin and Oxytocin Receptors, QSAR & Combinatorial Science, 2009, vol. 28, nr 10, s.1166-1175. DOI:10.1002/qsar.200810164
  • Ślusarz Magdalena, Ślusarz Rafał, Ciarkowski Jerzy: Molecular dynamics study of the internal water molecules in vasopressin and oxytocin receptors, Protein and Peptide Letters, 2009, vol. 16, nr 4, s.342-350
  • Errata
  • Bobrowski Maciej, Liwo Józef Adam, Hirao Kimihiko: Erratum: Theoretical study of the energetics of the reactions of triplet dioxygen with hydroquinone, semiquinone, and their protonated forms: relation to the mechanism of superoxide generation in the respiratory chain, Journal of Physical Chemistry B, 2009, vol. 113, nr 29, s.10049-10050. DOI:10.1021/jp905421z
  • 2008  
  • Kleinerman Dana S., Czaplewski Cezary, Liwo Józef Adam [i in.]: Implementations of Nosé-Hoover and Nosé-Poincare thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain, Journal of Chemical Physics, 2008, vol. 128, nr 24, s.1-17, Numer artykułu:245103. DOI:10.1063/1.2943146
  • Liwo Józef Adam, Czaplewski Cezary, Ołdziej Stanisław [i in.]: Computational techniques for efficient conformational sampling of proteins, Current Opinion in Structural Biology, 2008, vol. 18, nr 2, s.134-139. DOI:10.1016/j.sbi.2007.12.001
  • Makowska Joanna, Bagińska Katarzyna, Liwo Józef Adam, Chmurzyński Lech [i in.]: Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: Comparison between theory and experiment, Biopolymers, 2008, vol. 90, nr 5, s.724-732. DOI:10.1002/bip.21046
  • Makowska Joanna, Bagińska Katarzyna, Lewandowska Agnieszka, Liwo Józef Adam, Chmurzyński Lech [i in.]: Influence of charge and size of terminal amino-acid residues on local conformational states and shape of alanine-based peptides, Biopolymers, 2008, vol. 90, nr 6, s.772-782. DOI:10.1002/bip.21077
  • Makowski Mariusz, Sobolewski Emil, Liwo Józef Adam [i in.]: Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains, Journal of Physical Chemistry B, 2008, vol. 112, nr 36, s.11385-11395. DOI:10.1021/jp803896b
  • Ossowski Tadeusz, Liwo Józef Adam, Falkowski Piotr, Zarzeczańska Dorota [i in.]: Determination of the pKa values of some biologically active and inactive hydroxyquinones, Journal of the Brazilian Chemical Society, 2008, vol. 19, nr 1, s.175-183. DOI:10.1590/S0103-50532008000100025
  • Rodziewicz-Motowidło Sylwia, Czaplewski Cezary, Łuczak Sylwia, Ciarkowski Jerzy: Conformation-activity relationships of cyclo-constrained μ/δ opioid agonists derived from the N-terminal tetrapeptide segment of dermorphin/deltorphin, Journal of Peptide Science, 2008, vol. 14, nr 8, s.898-902. DOI:10.1002/psc.1022
  • Shen Hujun, Czaplewski Cezary, Liwo Józef Adam [i in.]: Implementation of a serial replica exchange method in a Physics-Based United-Residue (UNRES) force field, Journal of Chemical Theory and Computation, 2008, vol. 4, nr 8, s.1386-1400. DOI:10.1021/ct800063d
  • Sikorska Celina, Smuczyńska Sylwia, Skurski Piotr, Anusiewicz Iwona: BX4- and AlX4- superhalogen anions (X = F, Cl, Br): an ab initio study, Inorganic Chemistry, 2008, vol. 47, nr 16, s.7348-7354. DOI:10.1021/ic800863z
  • Skwierawska Agnieszka, Rodziewicz-Motowidło Sylwia, Ołdziej Stanisław, Liwo Józef Adam [i in.]: Conformational studies of the α-helical 28-43 fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus, Biopolymers, 2008, vol. 89, nr 11, s.1032-1044. DOI:10.1002/bip.21056
  • Zieleniak Agnieszka, Rodziewicz-Motowidło Sylwia, Rusak Łukasz, Czaplewski Cezary, Ciarkowski Jerzy [i in.]: Deltorphin analogs restricted via a urea bridge: structure and opioid activity, Journal of Peptide Science, 2008, vol. 14, nr 7, s.830-837. DOI:10.1002/psc.1010
  • 2007
  • Bobrowski Maciej, Liwo Józef Adam, Hirao Kimihiko: Theoretical study of the energetics of the reactions of triplet dioxygen with hydroquinone, semiquinone, and their protonated forms:  relation to the mechanism of superoxide generation in the respiratory chain, Journal of Physical Chemistry B, 2007, vol. 111, nr 13, s.3543-3549. DOI:10.1021/jp065603x
  • Chinchio M., Czaplewski Cezary, Liwo Józef Adam, Ołdziej Stanisław [i in.]: Dynamic formation and breaking of disulfide bonds in molecular dynamics simulations with the UNRES force field, Journal of Chemical Theory and Computation, 2007, vol. 3, nr 4, s.1236-1248. DOI:10.1021/ct7000842
  • Grajek Hanna, Liwo Józef Adam, Wiczk Wiesław [i in.]: Resolution of the excitation-emission spectra of FMN in rigid poly(vinyl alcohol) matrices, Journal of Photochemistry and Photobiology B-Biology, 2007, vol. 86, nr 3, s.193-198. DOI:10.1016/j.jphotobiol.2006.09.003
  • Kozłowska Urszula, Liwo Józef Adam, Scheraga Harold A. : Determination of virtual-bond-angle potentials of mean force for coarse-grained simulations of protein structure and folding from ab initio energy surfaces of terminally-blocked glycine, alanine, and proline, Journal of Physics-Condensed Matter, 2007, vol. 19, s.1-15, Numer artykułu:285203. DOI:10.1088/0953-8984/19/28/285203
  • Liwo Józef Adam, Czaplewski Cezary, Kalinowski Sebastian, Ołdziej Stanisław, Wachucik Katarzyna [i in.]: Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins, Journal of Physical Chemistry B, 2007, vol. 111, nr 1, s.260-285. DOI:10.1021/jp065380a
  • Makowska Joanna, Rodziewicz-Motowidło Sylwia, Bagińska Katarzyna, Makowski Mariusz, Liwo Józef Adam, Chmurzyński Lech [i in.]: Further evidence for the absence of polyproline II stretch in the XAO peptide, Biophysical Journal, 2007, vol. 92, nr 8, s.2904-2917. DOI:10.1529/biophysj.106.097550
  • Murarka Rajesh, Liwo Józef Adam, Scheraga Harold A. : Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone, Journal of Chemical Physics, 2007, vol. 127, nr 15, s.1-16, Numer artykułu:155103. DOI:10.1063/1.2784200
  • Niv Masha Y., Ripoll Daniel R., Liwo Józef Adam [i in.]: Topology of Type II REases revisited; structural classes and the common conserved core, Nucleic Acids Research, 2007, vol. 35, nr 7, s.2227-2237. DOI:10.1093/nar/gkm045
  • Rojas Ana V., Liwo Józef Adam, Scheraga Harold A. : Molecular dynamics with the united-residue force field: Ab initio folding simulations of multichain proteins, Journal of Physical Chemistry B, 2007, vol. 111, nr 1, s.293-309. DOI:10.1021/jp065810x
  • Scheraga Harold A. , Khalili Mey, Liwo Józef Adam: Protein-folding dynamics: overview of molecular simulation techniques, Annual Review of Physical Chemistry, 2007, vol. 58, s.57-83. DOI:10.1146/annurev.physchem.58.032806.104614
  • Witt Magdalena, Ciarkowski Jerzy, Czaplewski Cezary: Molecular simulations of rhodopsin tetrameter, Protein and Peptide Letters, 2007, vol. 14, nr 4, s.381-387. DOI:10.2174/092986607780363916
  • 2006  
  • Khalili Mey, Liwo Józef Adam, Scheraga Harold A. : Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains, Journal of Molecular Biology, 2006, vol. 355, nr 3, s.536-547. DOI:10.1016/j.jmb.2005.10.056
  • Liepina Inta, Czaplewski Cezary, Liwo Józef Adam [i in.]: Molecular dynamics study of amyloid formation of two Abl-SH3 domain peptides, Journal of Peptide Science, 2006, vol. 12, nr 12, s.780-789. DOI:10.1002/psc.813
  • Makowska Joanna, Bagińska Katarzyna, Makowski Mariusz, Liwo Józef Adam, Kasprzykowski Franciszek, Chmurzyński Lech [i in.]: Assessment of two theoretical methods to estimate potentiometric titration curves of peptides: comparison with experiment, Journal of Physical Chemistry B, 2006, vol. 110, nr 9, s.4451-4458. DOI:10.1021/jp054814j
  • Makowska Joanna, Rodziewicz-Motowidło Sylwia, Bagińska Katarzyna, Liwo Józef Adam, Chmurzyński Lech [i in.]: Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins, Proceedings of the National Academy of Sciences of the United States of America, 2006, vol. 103, nr 6, s.1744-1749. DOI:10.1073/pnas.0510549103
  • Rakowski Franciszek, Grochowski Paweł, Liwo Józef Adam [i in.]: Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function, Journal of Chemical Physics, 2006, vol. 125, nr 20, s.1-10, Numer artykułu:204107. DOI:10.1063/1.2399526
  • Sikorska Emilia, Ślusarz Magdalena, Lammek Bernard: Conformational studies of vasopressin analogues modified with N-methylphenylalanine enantiomers in dimethyl sulfoxide solution, Biopolymers, 2006, vol. 82, nr 6, s.603-614. DOI:10.1002/bip.20514
  • Sikorska Emilia, Ślusarz Magdalena, Ślusarz Rafał, Kowalczyk Wioleta, Lammek Bernard: Investigation of cis/trans ratios of peptide bonds in AVP analogues containing N-methylphenylalanine enantiomers, Journal of Peptide Science, 2006, vol. 12, nr 1, s.13-24. DOI:10.1002/psc.684
  • Ślusarz Magdalena, Giełdoń Artur, Ślusarz Rafał, Ciarkowski Jerzy: Analysis of interactions responsible for vasopressin binding to human neurohypophyseal hormone receptors - molecular dynamics study of the activated receptor-vasopressin-Gα systems, Journal of Peptide Science, 2006, vol. 12, nr 3, s.180-189. DOI:10.1002/psc.714
  • Ślusarz Magdalena, Ślusarz Rafał, Ciarkowski Jerzy: Investigation of mechanism of desmopressin binding in vasopressin V2 receptor versus vasopressin V1a and oxytocin receptors: molecular dynamics simulation of the agonist-bound state in the membrane-aqueous system, Biopolymers, 2006, vol. 81, nr 5, s.321-338. DOI:10.1002/bip.20420
  • Ślusarz Magdalena, Sikorska Emilia, Ślusarz Rafał, Ciarkowski Jerzy: Molecular docking-based study of vasopressin analogues modified at positions 2 and 3 with N-methylphenylalanine: influence on receptor-bound conformations and interactions with vasopressin and oxytocin receptors, Journal of Medicinal Chemistry, 2006, vol. 49, nr 8, s.2463-2469. DOI:10.1021/jm051075m
  • Ślusarz Magdalena, Ślusarz Rafał, Ciarkowski Jerzy: Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin - modeling of an activated state, Journal of Peptide Science, 2006, vol. 12, nr 3, s.171-179. DOI:10.1002/psc.713
  • Ślusarz Rafał, Ślusarz Magdalena, Lammek Bernard, Ciarkowski Jerzy: Molecular modeling of meta II rhodopsin, QSAR & Combinatorial Science, 2006, vol. 25, nr 2, s.105-113. DOI:10.1002/qsar.200430920
  • 2005
  • Ciarkowski Jerzy, Witt Magdalena, Ślusarz Rafał: A hypothesis for GPCR activation, Journal of Molecular Modeling, 2005, vol. 11, nr 4-5, s.407-415. DOI:10.1007/s00894-005-0270-9
  • Czaplewski Cezary, Kalinowski Sebastian, Liwo Józef Adam [i in.]: Comparison of two approaches to potential of mean force calculations of hydrophobic association: particle insertion and weighted histogram analysis methods, Molecular Physics, 2005, vol. 103, nr 21-23, s.3153-3167. DOI:10.1080/00268970500233797
  • Czaplewski Cezary, Liwo Józef Adam, Ripoll Daniel R. [i in.]: Molecular origin of anticooperativity in hydrophobic association, Journal of Physical Chemistry B, 2005, vol. 109, nr 16, s.8108-8119. DOI:10.1021/jp040691b
  • Khalili Mey, Liwo Józef Adam, Rakowski Franciszek [i in.]: Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode, Journal of Physical Chemistry B, 2005, vol. 109, nr 28, s.13785-13797. DOI:10.1021/jp058008o
  • Khalili Mey, Liwo Józef Adam, Jagielska Anna Maria [i in.]: Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model a-helical systems, Journal of Physical Chemistry B, 2005, vol. 109, nr 28, s.13798-13810. DOI:10.1021/jp058007w
  • Liwo Józef Adam, Khalili Mey, Scheraga Harold A. : Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains, Proceedings of the National Academy of Sciences of the United States of America, 2005, vol. 102, nr 7, s.2362-2367. DOI:10.1073/pnas.0408885102
  • Makowska Joanna, Bagińska Katarzyna, Kasprzykowski Franciszek, Liwo Józef Adam, Chmurzyński Lech [i in.]: Interplay of charge distribution and conformation in peptides: comparison of theory and experiment, Biopolymers, 2005, vol. 80, nr 2-3, s.214-224. DOI:10.1002/bip.20180
  • Makowska Joanna, Makowski Mariusz, Liwo Józef Adam, Chmurzyński Lech: Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean force, Journal of Computational Chemistry, 2005, vol. 26, nr 3, s.235-242. DOI:10.1002/jcc.20166
  • Ołdziej Stanisław, Czaplewski Cezary, Liwo Józef Adam, Makowski Mariusz, Kaźmierkiewicz Rajmund [i in.]: Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests, Proceedings of the National Academy of Sciences of the United States of America, 2005, vol. 102, nr 21, s.7547-7552. DOI:10.1073/pnas.0502655102
  • Ślusarz Magdalena, Giełdoń Artur, Ślusarz Rafał, Ciarkowski Jerzy [i in.]: Study of new oxytocin antagonist barusiban (Fe200 440) affinity toward human oxytocin receptor versus vasopressin V1a and V2 receptors - molecular dynamics simulation in POPC bilayer, QSAR & Combinatorial Science, 2005, vol. 24, nr 5, s.603-610. DOI:10.1002/qsar.200430919
  • Inna publikacja
  • Czaplewski Cezary, Kalinowski Sebastian, Liwo Józef Adam [i in.]: Reply to "Comment on 'Molecular origin of anticooperativity in hydrophobic association''', Journal of Physical Chemistry B, 2005, vol. 109, nr 44, s.21222-21224
  • 2004
  • Czaplewski Cezary, Liwo Józef Adam, Ołdziej Stanisław [i in.]: Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation, Polymer, 2004, vol. 45, nr 2, s.677-686. DOI:10.1016/j.polymer.2003.10.081
  • Czaplewski Cezary, Ołdziej Stanisław, Liwo Józef Adam [i in.]: Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds, Protein Engineering Design & Selection, 2004, vol. 17, nr 1, s.29-36. DOI:10.1093/protein/gzh003
  • Goulart Marília O.F., Falkowski Piotr, Ossowski Tadeusz, Liwo Józef Adam [i in.]: Electrochemical studies of isolapachol with emphasis on oxygen interaction with its radical anions, Journal of Electroanalytical Chemistry, 2004, vol. 566, nr 1, s.25-29. DOI:10.1016/j.jelechem.2003.10.043
  • Guzow Katarzyna, Ganzynkowicz Robert, Rzeska Alicja, Mrozek Justyna, Szabelski Mariusz, Liwo Józef Adam, Wiczk Wiesław [i in.]: Photophysical properties of tyrosine and its simple derivatives studied by time-resolved fluorescence spectroscopy, global analysis, and theoretical calculations, Journal of Physical Chemistry B, 2004, vol. 108, nr 12, s.3879-3889. DOI:10.1021/jp036721c
  • Khalili Mey, Liwo Józef Adam, Ołdziej Stanisław [i in.]: A united residue force-field for calcium-protein interactions, Protein Science, 2004, vol. 13, nr 10, s.2725-2735. DOI:10.1110/ps.04878904
  • Liepina Inta, Czaplewski Cezary, Liwo Józef Adam [i in.]: Towards gelsolin amyloid formation, Biopolymers, 2004, vol. 76, nr 6, s.543-548. DOI:10.1002/bip.20175
  • Liwo Józef Adam, Arłukowicz Piotr, Ołdziej Stanisław, Czaplewski Cezary, Makowski Mariusz [i in.]: Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 1. Tests of the approach using simple lattice protein models, Journal of Physical Chemistry B, 2004, vol. 108, nr 43, s.16918-16933. DOI:10.1021/jp040327c
  • Liwo Józef Adam, Ołdziej Stanisław, Czaplewski Cezary, Kozłowska Urszula [i in.]: Parametrization of backbone−electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from ab initio energy surfaces of model systems, Journal of Physical Chemistry B, 2004, vol. 108, nr 27, s.9421-9438. DOI:10.1021/jp030844f
  • Makowska Joanna, Makowski Mariusz, Giełdoń Artur, Liwo Józef Adam, Chmurzyński Lech: Theoretical calculations of heteroconjugation equilibrium constants in systems modeling acid - Base interactions in side chains of biomolecules using the potential of mean force, Journal of Physical Chemistry B, 2004, vol. 108, nr 32, s.12222-12230. DOI:10.1021/jp048116v
  • Malicka Joanna, Czaplewski Cezary, Groth Małgorzata, Wiczk Wiesław, Ołdziej Stanisław, Łankiewicz Leszek, Ciarkowski Jerzy, Liwo Józef Adam: Use of NMR and fluorescence spectroscopy as well as theoretical conformational analysis in conformation-activity studies on cyclic enkephalin analogues, Current Topics in Medicinal Chemistry, 2004, vol. 4, nr 1, s.123-133. DOI:10.2174/1568026043451591
  • Ołdziej Stanisław, Liwo Józef Adam, Czaplewski Cezary [i in.]: Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 2. Off-lattice tests of the method with single proteins, Journal of Physical Chemistry B, 2004, vol. 108, nr 43, s.16934-16949. DOI:10.1021/jp0403285
  • Ołdziej Stanisław, Łągiewka Justyna, Liwo Józef Adam, Czaplewski Cezary [i in.]: Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 3. Use of many proteins in optimization, Journal of Physical Chemistry B, 2004, vol. 108, nr 43, s.16950-16959. DOI:10.1021/jp040329x
  • Ślusarz Magdalena, Ślusarz Rafał, Ciarkowski Jerzy [i in.]: Molecular dynamics of complexes of atosiban with neurohypophyseal receptors in the fully hydrated phospholipid bilayer, QSAR & Combinatorial Science, 2004, vol. 23, nr 7, s.536-545. DOI:10.1002/qsar.200430888
  • Ślusarz Rafał, Ciarkowski Jerzy: Interaction of class A G protein-coupled receptors with G proteins, Acta Biochimica Polonica, 2004, vol. 51, nr 1, s.129-136. DOI:10.18388/abp.2004_3604
  • Errata
  • Czaplewski Cezary, Rodziewicz-Motowidło Sylwia, Dąbal Magdalena, Liwo Józef Adam [i in.]: Erratum to "Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles" [Biophys. Chem. 105 (2003) 339-359], Biophysical Chemistry, 2004, vol. 111, nr 3, s.267-271. DOI:10.1016/j.bpc.2004.07.001
  • 2003
  • Czaplewski Cezary, Rodziewicz-Motowidło Sylwia, Da̧bal Magdalena, Liwo Józef Adam [i in.]: Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles, Biophysical Chemistry, 2003, vol. 105, nr 2-3, s.339-359. DOI:10.1016/S0301-4622(03)00085-1
  • Giełdoń Artur, Kaźmierkiewicz Rajmund, Ślusarz Rafał, Ciarkowski Jerzy [i in.]: Molecular dynamics study of 4-OH-phenylacetyl-D-Y-(Me FQNRPR-NH2 selectivity to V1a receptor, Journal of Molecular Modeling, 2003, vol. 9, s.372-378. DOI:10.1007/s00894-003-0142-0
  • Goulart Marília O.F., Falkowski Piotr, Ossowski Tadeusz, Liwo Józef Adam [i in.]: Electrochemical study of oxygen interaction with lapachol and its radical anions, Bioelectrochemistry, 2003, vol. 59, nr 1-2, s.85-87. DOI:10.1016/S1567-5394(03)00005-7
  • Liepina Inta, Czaplewski Cezary, Liwo Józef Adam [i in.]: Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate, Biopolymers, 2003, vol. 71, nr 1, s.49-70. DOI:10.1002/bip.10375
  • Liepina Inta, Czaplewski Cezary, Liwo Józef Adam [i in.]: Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain, Journal of Molecular Structure-Theochem, 2003, vol. 630, nr 1-3, s.309-313. DOI:10.1016/S0166-1280(03)00159-3
  • Maksimiak Katarzyna, Rodziewicz-Motowidło Sylwia, Czaplewski Cezary, Liwo Józef Adam [i in.]: Molecular simulation study of the potentials of mean force for the interactions between models of like-charged and between charged and nonpolar amino acid side chains in water, Journal of Physical Chemistry B, 2003, vol. 107, nr 48, s.13496-13504. DOI:10.1021/jp030691w
  • Ołdziej Stanisław, Kozłowska Urszula, Liwo Józef Adam [i in.]: Determination of the potentials of mean force for rotation about Cα-Cα virtual bonds in polypeptides from the ab initio energy surfaces of terminally blocked glycine, alanine, and proline, Journal of Physical Chemistry A, 2003, vol. 107, nr 40, s.8035-8046. DOI:10.1021/jp0223410
  • Ślusarz Magdalena, Ślusarz Rafał, Kaźmierkiewicz Rajmund, Ciarkowski Jerzy [i in.]: Molecular modeling of the neurohypophyseal receptor/atosiban complexes, Protein and Peptide Letters, 2003, vol. 10, nr 3, s.295-302. DOI:10.2174/0929866033478898
  • Ślusarz Rafał, Ślusarz Magdalena, Kaźmierkiewicz Rajmund, Lammek Bernard: Molecular modeling of interaction of the vasopressin analogs with vasopressin and oxytocin receptors, QSAR & Combinatorial Science, 2003, vol. 22, nr 8, s.865-872. DOI:10.1002/qsar.200330839
  • Errata
  • Kaźmierkiewicz Rajmund, Liwo Józef Adam, Scheraga Harold A. : Erratum: Addition of side chains to a known backbone with defined side-chain centroids (Biophysical Chemistry (2003) 100 (261-280) PII: S0301462202002855), Biophysical Chemistry, 2003, vol. 106, nr 1, s.91-91. DOI:10.1016/S0301-4622(03)00245-X
  • 2002
  • Bobrowski Maciej, Liwo Józef Adam, Ołdziej Stanisław, Ossowski Tadeusz [i in.]: Ab initio study of the mechanism of singlet-dioxygen addition to hydroxyaromatic compounds: negative evidence for the involvement of peroxa and endoperoxide intermediates, Journal of Computational Chemistry, 2002, vol. 23, nr 11, s.1076-1089. DOI:10.1002/jcc.10102
  • Brzozowski Krzysztof, Łęgowska Anna, Rodziewicz-Motowidło Sylwia, Liwo Józef Adam, Rolka Krzysztof: The study of conformational equilibrium of c[Gln-Trp-Phe-Gly-Leu-Met], a NK-2 tachykinin antagonist, Polish Journal of Chemistry, 2002, vol. 76, nr 6, s.807-814
  • Czaplewski Cezary, Liwo Józef Adam, Rodziewicz-Motowidło Sylwia [i in.]: Can cooperativity in hydrophobic association be reproduced correctly by implicit solvation models?, International Journal of Quantum Chemistry, 2002, vol. 88, nr 1, s.41-55. DOI:10.1002/qua.10077
  • Czaplewski Cezary, Rodziewicz-Motowidło Sylwia, Liwo Józef Adam [i in.]: Comment on "anti-cooperativity in hydrophobic interactions: A simulation study of spatial dependence of three-body effects and beyond" [J. Chem. Phys. 115, 1414 (2001)], Journal of Chemical Physics, 2002, vol. 116, nr 6, s.2665-2667. DOI:10.1063/1.1434994
  • Kaźmierkiewicz Rajmund, Liwo Józef Adam, Scheraga Harold A. : Addition of side chains to a known backbone with defined side-chain centroids, Biophysical Chemistry, 2002, vol. 100, nr 1-3, s.261-280. DOI:10.1016/S0301-4622(02)00285-5
  • Kaźmierkiewicz Rajmund, Liwo Józef Adam, Scheraga Harold A. : Energy-based reconstruction of a protein backbone from its α-carbon trace by a Monte-Carlo method, Journal of Computational Chemistry, 2002, vol. 23, nr 7, s.715-723. DOI:10.1002/jcc.10068
  • Liwo Józef Adam, Arłukowicz Piotr, Czaplewski Cezary, Ołdziej Stanisław [i in.]: A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field, Proceedings of the National Academy of Sciences of the United States of America, 2002, vol. 99, nr 4, s.1937-1942. DOI:10.1073/pnas.032675399
  • Malicka Joanna, Groth Małgorzata, Czaplewski Cezary, Wiczk Wiesław, Liwo Józef Adam: Conformational studies of cyclic enkephalin analogues with L- or D-proline in position 3, Biopolymers, 2002, vol. 63, nr 4, s.217-231. DOI:10.1002/bip.10068
  • Rodziewicz-Motowidło Sylwia, Brzozowski Krzysztof, Łęgowska Anna, Liwo Józef Adam, Rolka Krzysztof [i in.]: Conformational solution studies of neuropeptide γ using CD and NMR spectroscopy, Journal of Peptide Science, 2002, vol. 8, nr 5, s.211-226. DOI:10.1002/psc.384
  • Scheraga Harold A. , Liwo Józef Adam, Czaplewski Cezary [i in.]: Evolution of physics-based methodology for exploring the conformational energy landscape of proteins, Journal of Computational Chemistry, 2002, vol. 23, nr 1, s.28-34. DOI:10.1002/jcc.1154
  • 2001
  • Ciarkowski Jerzy, Drabik Piotr, Giełdoń Artur, Kaźmierkiewicz Rajmund, Ślusarz Rafał: Signal transmission via G protein-coupled receptors in the light of rhodopsin structure determination, Acta Biochimica Polonica, 2001, vol. 48, nr 4, s.1203-1207. DOI:10.18388/abp.2001_3892
  • Drabik Piotr, Liwo Józef Adam, Czaplewski Cezary, Ciarkowski Jerzy: The investigation of the effects of counterions in protein dynamics simulations, Protein Engineering, 2001, vol. 14, nr 10, s.747-752. DOI:10.1093/protein/14.10.747
  • Giełdoń Artur, Kaźmierkiewicz Rajmund, Ślusarz Rafał, Ciarkowski Jerzy: Molecular modeling of interactions of the non-peptide antagonist YM087 with the human vasopressin V1a, V2 receptors and with oxytocin receptors, Journal of Computer-Aided Molecular Design, 2001, vol. 15, s.1085-1104. DOI:10.1023/A:1015905822671
  • Groth Małgorzata, Malicka Joanna, Rodziewicz-Motowidło Sylwia, Czaplewski Cezary, Klaudel Lidia, Wiczk Wiesław, Liwo Józef Adam: Determination of conformational equilibrium of peptides in solution by NMR spectroscopy and theoretical conformational analysis: application to the calibration of mean-field solvation models, Biopolymers, 2001, vol. 60, nr 2, s.79-95
  • Liwo Józef Adam, Czaplewski Cezary, Pillardy Jarosław [i in.]: Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field, Journal of Chemical Physics, 2001, vol. 115, nr 5, s.2323-2347. DOI:10.1063/1.1383989
  • Malicka Joanna, Ganzynkowicz Robert, Groth Małgorzata, Czaplewski Cezary, Liwo Józef Adam, Wiczk Wiesław [i in.]: Fluorescence decay time distribution analysis of cyclic enkephalin analogues; Influence of solvent and Leu configuration in position 5 on conformation, Acta Biochimica Polonica, 2001, vol. 48, nr 1, s.95-102. DOI:10.18388/abp.2001_5115
  • Malicka Joanna, Groth Małgorzata, Czaplewski Cezary, Liwo Józef Adam, Wiczk Wiesław [i in.]: Influence of solvent and configuration of residues at positions 2 and 3 on distance and mobility of pharmacophore groups at positions 1 and 4 in cyclic enkephalin analogues, Biopolymers, 2001, vol. 59, nr 3, s.180-190
  • Malicka Joanna, Groth Małgorzata, Czaplewski Cezary, Liwo Józef Adam, Wiczk Wiesław [i in.]: Influence of solvents and leucine configuration at position 5 on tryptophan fluorescence in cyclic enkephalin analogues, Biopolymers, 2001, vol. 58, nr 4, s.447-457
  • Pillardy Jarosław, Czaplewski Cezary, Liwo Józef Adam, Arłukowicz Piotr, Ołdziej Stanisław [i in.]: Development of physics-based energy functions that predict medium-resolution structures for proteins of the α, β, and α/β structural classes, Journal of Physical Chemistry B, 2001, vol. 105, nr 30, s.7299-7311. DOI:10.1021/jp0111012
  • Pillardy Jarosław, Czaplewski Cezary, Liwo Józef Adam, Kaźmierkiewicz Rajmund, Ołdziej Stanisław [i in.]: Recent improvements in prediction of protein structure by global optimization of a potential energy function, Proceedings of the National Academy of Sciences of the United States of America, 2001, vol. 98, nr 5, s.2329-2333. DOI:10.1073/pnas.041609598
  • Rodziewicz-Motowidło Sylwia, Lesner Adam, Łęgowska Anna, Czaplewski Cezary, Liwo Józef Adam, Rolka Krzysztof [i in.]: Synthesis, activity on NK-3 tachykinin receptor and conformational solution studies of scyliorhinin II analogs modified at position 16, JOURNAL OF PEPTIDE RESEARCH, 2001, vol. 58, nr 2, s.159-172. DOI:10.1034/j.1399-3011.2001.00886.x
  • Ślusarz Rafał, Kaźmierkiewicz Rajmund, Giełdoń Artur, Lammek Bernard, Ciarkowski Jerzy: Molecular docking-based test for affinities of two ligands toward vasopressin and oxytocin receptors, Acta Biochimica Polonica, 2001, vol. 48, nr 1, s.131-135. DOI:10.18388/abp.2001_5119
  • 2000
  • Bobrowski Maciej, Liwo Józef Adam, Ołdziej Stanisław, Ossowski Tadeusz [i in.]: CAS MCSCF/CAS MCQDPT2 study of the mechanism of singlet oxygen addition to 1,3-butadiene and benzene, Journal of the American Chemical Society, 2000, vol. 122, nr 34, s.8112-8119. DOI:10.1021/ja001185c
  • Czaplewski Cezary, Rodziewicz-Motowidło Sylwia, Liwo Józef Adam [i in.]: Molecular simulation study of cooperativity in hydrophobic association, Protein Science, 2000, vol. 9, nr 6, s.1235-1245. DOI:10.1110/ps.9.6.1235
  • Drabik Piotr, Czaplewski Cezary, Kasprzykowski Franciszek, Łankiewicz Leszek, Ciarkowski Jerzy [i in.]: Theoretical studies of binding modes of two covalent inhibitors of cysteine proteases, Acta Biochimica Polonica, 2000, vol. 47, nr 4, s.1061-1066. DOI:10.18388/abp.2000_3959
  • Klaudel Lidia, Rodziewicz-Motowidło Sylwia, Liwo Józef Adam, Rolka Krzysztof: A comparison of solution conformations of scyliorhinin I and its analogue with N-methyl-L-phenylalanine in position 7, Polish Journal of Chemistry, 2000, vol. 74, nr 8, s.1091-1099
  • Lee Jooyoung, Pillardy Jarosław, Liwo Józef Adam [i in.]: Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals, Computer Physics Communications, 2000, vol. 128, nr 1-2, s.399-411. DOI:10.1016/S0010-4655(99)00515-9
  • Lee Jooyoung, Liwo Józef Adam, Ripoll Daniel R. [i in.]: Hierarchical energy-based approach to protein-structure prediction: blind-test evaluation with CASP3 targets, International Journal of Quantum Chemistry, 2000, vol. 77, nr 1, s.90-117
  • Ossowski Tadeusz, Pipka Piotr, Liwo Józef Adam [i in.]: Electrochemical and UV-spectrophotometric study of oxygen and superoxide anion radical interaction with anthraquinone derivatives and their radical anions, Electrochimica Acta, 2000, vol. 45, nr 21, s.3581-3587. DOI:10.1016/S0013-4686(00)00479-5
  • Rodziewicz-Motowidło Sylwia, Łęgowska Anna, Qi Xiao-Fei, Czaplewski Cezary, Liwo Józef Adam, Rolka Krzysztof [i in.]: Solution conformational study of Scyliorhinin I analogues with conformational constraints by two-dimensional NMR and theoretical conformational analysis, JOURNAL OF PEPTIDE RESEARCH, 2000, vol. 56, nr 3, s.132-146. DOI:10.1034/j.1399-3011.2000.00697.x
Pokaż rejestr zmian
Data publikacji: piątek, 28. luty 2014 - 21:35; osoba wprowadzająca: Magdalena Ślusarz Ostatnia zmiana: środa, 9. Listopad 2022 - 11:32; osoba wprowadzająca: Magdalena Ślusarz