Publikacje | Wydział Chemii

Publikacje Pracowni Modelowania Molekularnego

2018

  1. Karczyńska AS, Mozolewska MA, Krupa P, Giełdoń A, Liwo A, Czaplewski C. 10. "Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information" Proteins. 2018 86, 228-239.
  2. Krupa P, Hałabis A, Żmudzińska W, Ołdziej S, Scheraga HA, Liwo A. "Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics" J Chem Inf Model. 2018, 58, 206.
  3. Grzeszczuk MJ, Bąk A, Banaś AM, Urbanowicz P, Dunin-Horkawicz S, Gieldon A, Czaplewski C, Liwo A, Jagusztyn-Krynicka EK. "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, 13, e0195358.
  4. Czaplewski C, Karczynska A, Sieradzan AK, Liwo A. "UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics" Nucleic Acids Res. 2018 Jul 2;46, W304-W309.
  5. Karczyńska A, Mozolewska MA, Krupa P, Giełdoń A, Bojarski KK, Zaborowski B, Liwo A, Ślusarz R, Ślusarz M, Lee J, Joo K, Czaplewski C. "Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets" J Mol Graph Model. 2018 83, 92-99.
  6. Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Giełdoń A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Ślusarz M, Ślusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popović Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Ołdziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D; Foldit Players consortium, Crivelli SN. "An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12" Sci Rep. 2018 8, 9939.
  7. Sieradzan AK, Golon Ł, Liwo A. "Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing" Phys Chem Chem Phys. 2018 20, 19656-19663.
  8. Kohut G, Liwo A, Bősze S, Beke-Somfai T, Samsonov SA. Protein-Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges For Flexible Systems. J Phys Chem B. 2018, 122, 7821-7827
  9. Vallet SD, Miele AE, Uciechowska-Kaczmarzyk U, Liwo A, Duclos B, Samsonov SA, Ricard-Blum S. "Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners." Sci Rep. 2018, 8, 11768.
  10. Sieradzan AK, Giełdoń A, Yin Y, He Y, Scheraga HA, Liwo A. A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields. J Comput Chem. 2018, 39, 2360-2370.

2017

  1. Mozolewska MA, Sieradzan AK, Niadzvedstki A, Czaplewski C, Liwo A, Krupa P. "Role of the sulfur to α-carbon thioether bridges in thurincin H", J Biomol Struct Dyn. 2017, 35, 2868-2879.
  2. Krupa P, Hałabis A, Żmudzińska W, Ołdziej S, Scheraga HA, Liwo A. "Maximum likelihood calibration of the UNRES force field for simulation of protein structure and dynamics" J Chem Inf Model. 2017, doi: 10.1021/acs.jcim.7b00716
  3. Johnston T, Zhang B, Liwo A, Crivelli S, Taufer M. "In situ data analytics and indexing of protein trajectories" J Comput Chem. 2017, 38,1419-1430.
  4. Karczyńska AS, Czaplewski C, Krupa P, Mozolewska MA, Joo K, Lee J, Liwo A. "Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian Replica Exchange coarse-grained molecular dynamics simulations of proteins" J Comput Chem. 2017 38, 2730-2746.
  5. Krupa P, Sieradzan AK, Mozolewska MA, Li H, Liwo A, Scheraga HA. "Dynamics of disulfide-bond disruption and formation in the thermal unfolding of ribonuclease A" J Chem Theory Comput. 2017, 13:5721-5730.
  6. Lubecka EA, Liwo A. "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" J Chem Phys. 2017 147, 115101.
  7. Sieradzan AK, Makowski M, Augustynowicz A, Liwo A. "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" J Chem Phys. 2017 1462):124106.

2016

  1. Krupa P, Mozolewska MA, Wiśniewska M, Yin Y, He Y, Sieradzan AK, Ganzynkowicz R, Lipska AG, Karczyńska A, Ślusarz M, Ślusarz R, Giełdoń A, Czaplewski C, Jagieła D, Zaborowski B, Scheraga HA, Liwo A. "Performance of protein-structure predictions with the physics-based UNRES force field in CASP11" Bioinformatics, 2016 Jul 4. pii: btw404
  2. Lipska AG, Seidman SR, Sieradzan AK, Giełdoń A, Liwo A, Scheraga HA. "Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction", J Chem Phys. 2016, 144, 184110.
  3. Gieldon A, Zurawa-Janicka D, Jarzab M, Wenta T, Golik P, Dubin G, Lipinska B, Ciarkowski J. "Distinct 3D Architecture and Dynamics of the Human HtrA2(Omi) Protease and Its Mutated Variants", PLoS One. 2016, 11:e0161526.
  4. Lubecka EA, Sikorska E, Sobolewski D, Prahl A, Slaninová J, Ciarkowski J. "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 106, 245-59
  5. Jarzab M, Wenta T, Zurawa-Janicka D, Polit A, Gieldon AJ, Wysocka M, Glaza P, Skorko-Glonek J, Ciarkowski J, Lesner A, Lipinska B. "Intra- and intersubunit changes accompanying thermal activation of the HtrA2(Omi) protease homotrimer", Biochim Biophys Acta. 2016,1864, 283-96.

2015

  1. Yin Y, Sieradzan AK, Liwo A, He Y, Scheraga HA. "Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions", J Chem Theory Comput. 2015 11, 1792-808.
  2. He Y, Liwo A, Scheraga HA. "Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach", J Chem Phys. 2015 143, 243111
  3. Zaborowski B, Jagieła D, Czaplewski C, Hałabis A, Lewandowska A, Żmudzińska W, Ołdziej S, Karczyńska A, Omieczynski C, Wirecki T, Liwo A. "A Maximum-Likelihood Approach to Force-Field Calibration", J Chem Inf Model. 2015 55, 2050-70.
  4. Wiśniewska M, Sobolewski E, Ołdziej S, Liwo A, Scheraga HA, Makowski M. "Theoretical Studies of Interactions between O-Phosphorylated and Standard Amino-Acid Side-Chain Models in Water", J Phys Chem B. 2015, 119, 8526-34.
  5. Yin Y, Sieradzan AK, Liwo A, He Y, Scheraga HA. "Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions", J Chem Theory Comput. 2015, 11, 1792-808.
  6. Sieradzan AK, Krupa P, Scheraga HA, Liwo A, Czaplewski C. "Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the united residue (UNRES) force field for protein simulations", J Chem Theory Comput. 2015, 2, 817-831.
  7. Ślusarz MJ. "Vasopressin V1a and V1b receptor modulators: a patent review (2012 - 2014)", Expert Opin Ther Pat. 2015, 6, 711-722.
  8. Gołaś EI, Czaplewski C, Scheraga HA, Liwo A. "Common functionally important motions of the nucleotide-binding domain of Hsp70", Proteins. 2015, 83, 282-99.
  9. Lipska AG, Sieradzan AK, Krupa P, Mozolewska MA, D'Auria S, Liwo A. "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", J Mol Model. 2015, 64. DOI: 10.1007/s00894-015-2609-1
  10. Krupa P, Mozolewska MA, Joo K, Lee J, Czaplewski C, Liwo A. "Prediction of protein structure by template-based modeling combined with the UNRES force field", J Chem Inf Model. 2015, w druku
  11. Mozolewska MA, Krupa P, Scheraga HA, Liwo A. "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. 2015, w druku DOI: 10.1002/prot.24824.
  12. Lubecka EA, Sikorska E, Sobolewski D, Prahl A, Slaninová J, Ciarkowski J. "Arginine-, D-arginine-vasopressin, and their inverso analogues in micellar and liposomic models of cell membrane: CD, NMR, and molecular dynamics studies", Eur Biophys J. 2015, 44, 727-43.
  13. Maszota M, Karska N, Spodzieja M, Ciarkowski J, Kołodziejczyk AS, Rodziewicz-Motowidło S, Czaplewska P. "Structural studies of the C-terminal 19-peptide of serum amyloid A and its Pro → Ala variants interacting with human cystatin C" J Mol Recognit. 2015, 28, 413-26

2014

  1. Figaj, D., Giełdoń, A., Polit, A., Sobiecka-Szkatuła, A., Koper, T., Denkiewicz, M., Banecki, B., Lesner, A., Ciarkowski, J., Lipinska B., Skorko-Glonek, J. “The LA Loop as an Important Regulatory Element of the HtrA (DegP) Protease from Escherichia coli; Structural and Functional Studies”, J. Biol. Chem., 2014, 289, 15880–15893.  
  2. Khoury, G.A., Liwo, A., Khatib, F., Zhou, H., Chopra, G., Bacardit, J., Bortot, L.O., Faccioli, R.A., Deng, X., He, Y., Krupa, P., Li, J., Mozolewska, M.A., Sieradzan, A.K., Smadbeck, J., Wirecki, T., Cooper, S., Flatten, J., Xu, K., Baker, D., Cheng, J., Delbem, A.C.B., Floudas, C.A., Keasar, C., Levitt, M., Popović, Z., Scheraga, H.A., Skolnick, J., Crivelli, S.N. and Foldit Players. "WeFold: A coopetition for protein structure prediction", Proteins: Struct. Funct. Bioinfo., 2014, 82, 1850-1868.
  3. Liwo, A., Baranowski, M., Czaplewski, C., Gołaś, E., He, Y., Jagieła, D., Krupa, P., Maciejczyk, M., Makowski, M., Mozolewska, M.A., Niadzvedtski, A., Ołdziej, S., Scheraga, H.A., Sieradzan, A.K., Ślusarz, R., Wirecki, T., Yin, Y., Zaborowski, B. "A unified coarse-grained model of biological macromolecules based on mean-field multipole.multipole interactions", J. Molec. Model., 2014, 20, 1-15.
  4. Kachlishvili, K., G.G. Maisuradze, G.G., Martin, O.A, Liwo, A., Vila, J.A., Scheraga, H.A. "Accounting for a mirror-image conformation as a subtle effect in protein folding". Proc. Natl. Acad. Sci. USA, 2014, 111, 8458-8463.
  5. Sieradzan, A.K., Niadzvedtski, A., Scheraga, H.A., Liwo, A. "Revised backbone-virtual-bond-angle potentials to treat the L- and D-amino acid residues in the coarse-grained united residue (UNRES) force field", J. Chem. Theory Comput., 2014, 10, 2194-2203.
  6. Krokhotin, A., Liwo, A., Maisuradze, G.G., Niemi, H.J., Scheraga, HA. "Kinks, loopas and protein folding, with protein A as an example", J. Chem . Phys., 2014, 140, 025101
  7. Contreras-Romo, M.C., Martínez-Archundia, M., Deeb, O., Ślusarz, M.J., Ramírez-Salinas, G., Garduno-Juárez, R., Quintanar-Stephano, A., Ramírez-Galicia, G., Correa-Basurto, J. "Exploring the ligand recognition properties of the human vasopressin V1a receptor using QSAR and molecular modeling studies", Chem. Biol. Drug. Des., 2014, 83, 207-223.
  8. Contreras-Romo, M.C, Correa-Basurto, J., Padilla-Martínez, I., Martínez-Archundia, M., Martínez-Ramos, F., Ślusarz, M.J., López-Pérez, G., Quintanar-Stephano, A. "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", Med. Chem. Res., 2014, 23, 1581-1590.
  9. Gołaś, E.I., Czaplewski, C. "Computational simulation and analysis of a candidate for the design of a novel silk-based polymer". Biopolymers, 2014, 101, 915-923.

2013

  1. Liwo, A. "Coarse graining: a tool for large-scale simulations or more?" Phys. Scr., 2013, 87, 058502
  2. Maisuradze, G., Liwo, A., Senet, P., Scheraga, H.A. Local vs global motions in protein folding, J. Chem. Theory Comput., 2013, 9, 2907-2921.
  3. Ślusarz, M.J, Sikorska E., Ślusarz, R. "Interactions of vasopressin and oxytocin receptors with vasopressin analogues substituted in position 2 with 3,3'-diphenylalanine - a molecular docking study J. Pept. Sci., 2013, 19, 118-126.
  4. He, Y., Maciejczyk, M., Ołdziej, S., Scheraga, H.A., Liwo, A. "Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix, Phys. Rev. Lett., 2013, 110, 098101.
  5. Mozolewska, M., Krupa, P. "Zastosowanie pola gruboziarnistego UNRES do symulacji dynamiki molekularnej kompleksów białek na przykładzie drożdżowych białek opiekuńczych" w "Młodzi naukowcy dla polskiej nauki" red. Marcin Kuczera, Kraków 2013, 11, 139-143.
  6. Krupa, P., Sieradzan, A.K., Rackovsky, S., Baranowski, M., Ołdziej, S., Scheraga, H.A., Liwo, A., Czaplewski C."Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states" J. Chem. Teor. Comp. 2013, 9, 4620-4632.
  7. Maszota, M., Czaplewska, P., Karska, N., Spodzieja, M., Ciarkowski, J., Rodziewicz-Motowidło, S. "Consequence of ProAla point mutations for peptide structure and flexibility based on the SAA protein (86-104) fragment mutants. Peptides 2012. Proceedings of the 32th European Peptide Symposium, red. G. Kokotos, V. Constantinou-Kokotou, J. Matsoukas, The European Peptide Society 2013, 528-529.
  8. Lubecka, E.A., Sikorska, E., Kasprzykowski, F., Sobolewski, D., Ciarkowski, J. "Vasopressin and vasotocin - NMR studies in a membrane-mimicking environment" in Peptides 2012. Proceedings of the 32th European Peptide Symposium, red. G. Kokotos, V. Constantinou-Kokotou, J. Matsoukas, The European Peptide Society 2013, 564-565.
  9. Żurawa-Janicka, D., Jarząb, M., Polit, A., Skorko-Glonek, J., Lesner, A., Gitlin, A., Giełdoń, A., Ciarkowski, J., Glaza, P., Lubomska, A., Lipinska, B. "Temperature-induced changes of HtrA2(Omi) protease activity and structure" Cell Stress and Chaperones, 2013, 18, 35-51.
  10. He, Y., Mozolewska, M., Krupa, P., Sieradzan, A.K., Wirecki, T.K., Liwo, A., Kachlishvili, K., Rackovsky, S., Jagieła, D., Ślusarz, R., Czaplewski, C.R., Ołdziej, S., Scheraga, H.A. "Lessons from application of the UNRES force field to predictions of structures of CASP10 targets" PNAS, 2013, 110, 14936-14941.
  11. Krupa, P., Mozolewska, M., Maisuradze G., Liwo, A., Scheraga, H.A. i"Badanie procesu zwijania białek przy użyciu pola gruboziarnistego UNRES na podstawie peptydu 1EOL (domena WW) i jego mutantów" w "Młodzi naukowcy dla polskiej nauki", red. Marcin Kuczera, Kraków 2013, 11, 213-219.
  12. Mozolewska, M., "Dokowanie molekularne" w "Nowe trendy w naukach przyrodniczych 4", red. Marcin Kuczera, Creative Science, Kraków 2013, tom 1, 125-133.
  13. Lipinska, N., Zietkiewicz, S., Sobczak, A., Jurczyk, A., Potocki, W., Morawiec, E., Wawrzycka, A., Gumowski, K., Ślusarz, M., Rodziewicz-Motowidlo, S., Chrusciel, E., Liberek, K. "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", J. Biol Chem., 2013, 2857-286.

2012

  1. Makowska, M., Liwo, A., Chmurzyński, L., Scheraga, H.A. "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)" J. Sol. Chem., 2012, 41, 1738-1746.
  2. Lapidus, D., Duka, V., Stonkus, V., Czaplewski, C., Liwo, A., Ventura, S., Liepina, I. "Multiple beta-sheet molecular dynamics of amyloid formation from two Abl-SH3 domain peptides" Biopolymers (Pept. Sci.), 2012, 98 , 557-566
  3. Lubecka, E.A., Ciarkowski, J., Prahl, A., Sikorska, E. "Highly potent antidiuretic antagonists: conformational studies of vasopressin analogues modified with 1-naphthylalanine enantiomers at position 2", Chem. Biol. Drug Des. 2012, 79, 1033-1042.
  4. Dziadziuszko, H., Kumirska, J., Muza, S., Czerwicka, M., Lubecka, E.A., Stepnowski, P., Kunikowska, D. "Immunochemical studies of Salmonella Dakar and Salmonella Telaviv O-antigens (serogroup O:28)", FEMS Microbiol. Lett. 2012, 326, 55-61.
  5. Makowska, J., Liwo, A., Żmudzińska, W., Lewandowska, A., Chmurzyński, L., Scheraga, H.A. "Like-charged residues at the ends of oligoalanine sequences might induce a chain reversal", Biopolymers, 2012, 97, 240-249.
  6. Yin, Y., Maisuradze, G.G., Liwo, A., Scheraga, H.A. "Hidden protein folding pathways in free-energy landscapes uncovered by network analysis", J. Chem. Theory Comput., 2012, 8, 1176-1189.
  7. Sieradzan, A., Scheraga, H.A., Liwo, A. "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" J. Chem. Theor. Comput., 2012, 8, 1334-1343.
  8. Sobolewski, E., Oldziej, S., Wisniewska, A., Liwo, A., Makowski, M. "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", J. Phys. Chem. B, 2012, 23, 6844-6853.
  9. Haabis, A., Zmudzinska, W., Liwo, A., Oldziej, S. "Conformational dynamics of the Trp-Cage miniprotein at its folding temperature. J. Phys. Chem. B, 2012, 23, 6898-6907.
  10. Maisuradze, G.G., Zhou, R., Liwo, A., Xiao, Y., Scheraga. H.A. "Effects of Mutation, Truncation, and Temperature on the Folding Kinetics of a WW Domain", J. Mol. Biol., 2012, 420, 350-365.
  11. Sieradzan, A.K., Liwo, A., Hansmann, U.H.E. "Folding and self-assembly of a small protein complex", J. Chem. Theory Comput., 2012, 8, 3416-3422.
  12. Krokhotin, A., Liwo, A., Niemi, A.J., Scheraga, H.A. "Coexistence of phases in a protein heterodimer", J. Chem. Phys., 2012, 137, 035101.
  13. Sieradzan, A.K., Hansmann, U.H.E., Scheraga, H.A., Liwo, A. "Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues", J. Chem. Theory Comput., 2012, 8, 4746-47-4757.
  14. Gołaś, E., Maisuradze, G., Senet, P., Ołdziej, S., Czaplewski, C., Scheraga, H.A., Liwo, A. "Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics", J. Chem. Theory Comput., 2012 8, 1750-1764.
  15. Ołdziej, S., Czaplewski, C., Liwo, A., Vila, J.A., Scheraga, H.A. "Computing of structure, dynamics, and thermodynamics of proteins" in E.H. Egelman, editor: Comprehensive Biophysics, Vol 1, Biophysical Techniques for the Structural Characterization of Macromolecules, edited by H. J. Dyson. Oxford: Academic Press 2012, 494-513. ISBN 978-0123749208
  16. Ciarkowski, J., Łuczak, S., Jagieła, D., Sikorska, E., Wójcik, J., Oleszczuk, M., Izdebski, J. "Ensemble fits of restrained peptides' conformational equilibria to NMR data. Dependence on force fields: Amber/8 ff03 versus ECEPP/3", J. Mol. Graph. Model., 2012, 32, 67-74

2011

  1. Kumirska, J., Dziadziuszko, H., Czerwicka, M., Lubecka, E.A., Kunikowska, D., Siedlecka, E.M., Stepnowski, P. "The heterogenic structure of the O-antigenic part of Salmonella Telaviv lipopolysaccharide containing 3-acetamido-3,6-dideoxy-D-glucopyranose (serogroup O:28)" Biochemistry (Moscow) 2011, 76, 780-790
  2. Liepina, I., Czaplewski, C., Liwo, A., Duburs, G. 1,4-DHP-lipid parameters and rod like micellae, J. Biophys. Chem., 2011, 2, 386-394.
  3. Liwo, A., He, Y., Scheraga, H.A. "Coarse-grained force field: general folding theory" Phys. Chem. Chem. Phys., 2011, 13, 16890-16901.
  4. He, Y., Liwo, A., Weinstein, H., Scheraga, H.A. "PDZ Binding to the BAR Domain of PICK1 is Elucidated by Coarse-grained Molecular Dynamics", J. Mol. Biol., 2011, 405, 298-314.
  5. Makowski, M., Liwo, A., Sobolewski, E., Scheraga, H.A. "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" J. Phys. Chem. B, 2011, 115, 6119-6129.
  6. Makowski, M., Liwo, A., Scheraga, H.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" J. Phys. Chem. B, 2011, 115, 6130-6137.
  7. Rojas, A., Liwo, A., Scheraga, H.A. "A study of the alpha-helical intermediate preceding the aggregation of., the amino-terminal fragment of the beta-amyloid peptide (1-28)" J. Phys. Chem. B, 2011, 115, 12978-12983.
  8. Kamysz, E., Mickiewicz, B., Kamysz, W., Bielinska, S., Rodziewicz-Motowidlo, S., Ciarkowski, J. "Synthesis, biological activity and solution structure of new analogues of the antimicrobial Gramicidin S." J. Pept. Sci., 2011, 17, 211-217.
  9. Ślusarz, M.J. "Molecular modeling study of the opioid receptor interactions with series of cyclic deltorphin analogues", J. Pept. Sci., 2011, 17, 554-564.
  10. Ślusarz, R., Ślusarz, M.J., Samaszko, J., Madaj, J. "Conformational changes of peptidoglycan fragments during their interactions with vancomycin", Cent. Eur. J. Chem., 2011, 9, 422-431.
  11. Czaplewski, C., Liwo, A., Makowski, M., Ołdziej, S., Scheraga, H.A. "Coarse-Grained Models of Proteins: Theory and Applications", chapter 3 in Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies, edited by A. Koliński, Springer, 2011, 35-83.

2010

  1. Sobiecka-Szkatuła, A., Giełdoń, A., Scire, A., Tanfani, F., Figaj, D., Kper, T., Ciarkowski, J., Lipińska, B., Skorko-Glonek, J. "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, 500, 123-130.
  2. Lubecka, E., Sikorska, E., Kwiatkowska, A., Ciarkowski, J. "NMR Studies of Vasopressin Analogues Modified with Indoline-2-Carboxylic Acid in Position 2 in Dodecylphosphocholine Micelle" in Peptides 2010. Tales of Peptides. Proceedings of the 31th European Peptide Symposium, eds. Michal Lebl, Morten Medal, Knud J. Jensen, Thomas H?eg-Jensen, European Peptide Society 2010, pp. 428-429.
  3. Maszota, M., Czaplewska, P., Śladewska, A., Spodzieja, M., Ciarkowski, J. "NMR-Based Conformational Studies of the C-Terminal Heptadecapeptide(101-117) of Human Cystatin C" in Peptides 2010. Tales of Peptides. Proceedings of the 31th European Peptide Symposium, eds. Michal Lebl, Morten Medal, Knud J. Jensen, Thomas H?eg-Jensen, European Peptide Society 2010, pp. 594-595.
  4. Łuczak, S.L., Ciarkowski, J., Oleszczuk, M., Wójcik, J. "Ensemble Fit of Conformational Equilibria of Restrained Peptides to NMR Data. Dependence on Force Fields: Amber8 Vs ECEPP/3" in Peptides 2010. Tales of Peptides. Proceedings of the 31th European Peptide Symposium, eds. Michal Lebl, Morten Medal, Knud J. Jensen, Thomas H?eg-Jensen, European Peptide Society 2010, pp. 598-599.
  5. Lubecka, E., Kwiatkowska, A., Ciarkowski, J., Sikorska, E. "NMR studies of new arginine vasopressin analogs modified with ?-2-indanylglycine enantiomers at position 2 bound to sodium dodecyl sulfate micelles", Biophys. Chem. 2010, 151, 139-148.
  6. Kozak, M., Lewandowska, A., Ołdziej, S., Rodziewicz-Motowidło, S., Liwo, A. "Combination of SAXS and NMR techniques as a tool for the determination of peptide structure in solution." J. Phys. Chem. Letters, 2010, 1, 3128-3131.
  7. Kozłowska, U., Liwo, A., Scheraga, H.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. 1. The Method. J. Comput. Chem., 2010, 31, 1143-1153.
  8. Kozłowska, U.,Maisuradze, G.G., Liwo, A., Scheraga, H.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. 2. Results, comparison with statistical potentials, and implementation in the UNRES force field. J. Comput. Chem., 2010, 31, 1154-1167.
  9. Danalache, B., Gutkowska, J., Ślusarz, M.J., Berezowska, I., Jankowski, M. "Oxytocin-Gly-Lys-Arg: A Novel Cardiomyogenic Peptide", PLOS One, 2010, 5, e13643.
  10. Czaplewski, C., Liwo, A., Makowski, M., Scheraga, H.A. "Hydrophobic Interactions and Protein Folding", in Molecular Liquids Review Book, volume "Thermodynamics of Amino Acid and Protein Solutions", edited by J. Tsurko and W. Kunz, Transworld Research Network, 2010 ISBN 978-81-7895-473-8, w druku
  11. Ołdziej, S., Czaplewski, C., Liwo, A., Scheraga, H.A. "Towards temperature dependent coarse-grained potential of side-chain interactions for protein folding simulations, II. Simple functional forms for the side-chain-interaction potential: effect on simulated heat capacity and radius of gyration of staphylococcal protein A", BIBE, pp.263-266, IEEE International Conference on Bioinformatics and Bioengineering, Philadelphia, Pennsylvania USA, May 31-June 03, 2010. ISBN: 978-0-7695-4083-2
  12. Maisuradze, G., Senet, P., Czaplewski, C., Liwo, A., Scheraga, H.A. "Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field", J. Phys. Chem. A, 2010, 114, 4471-4485.
  13. Maisuradze, G.G., Liwo, A., Ołdziej, S., Scheraga, H.A. Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein. J. Am. Chem. Soc, 2010, 132, 9444-9452.
  14. Jagieła, D., Czaplewski, C., Liwo, A., Ołdziej, S., Scheraga, H.A. "Global parameter optimization of a physics-based united residue force field (UNRES) for proteins", inSiDE, Vol. 8 No. 1, eds. H-G. Hegering, T. Lippert, M. Resch, Gauss Centre for Supercomputing, 2010, 40-45.
  15. Makowski, M., Czaplewski, C., Liwo, A., Scheraga, H.A. "Potential of mean force of association of large hydrophobic particles: towards the nanoscale limit", J. Phys. Chem. B, 2010, 114, 993-1003.
  16. Liwo, A., Ołdziej, S., Czaplewski, C., Kleinerman, D., Blood P., Scheraga H.A. "Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics, J. Chem. Theory Comput., 2010, 6, 890-909.
  17. Sikorska, E., Kwiatkowska, A., Sobolewski, D., Ślusarz, R., Ślusarz, M.J. "Influence of bulky 3,3-diphenylalanine enantiomers replacing position 2 of AVP analogues on their conformations: NMR and molecular modeling studies" Eur. J. Med. Chem. , 2010, 45, 4065-4073.
  18. Ziętkiewicz, S., Ślusarz, M.J., Ślusarz, R., Liberek, K., Rodziewicz-Motowidło, S. "Conformational stability of the full-atom hexameric model of the ClpB chaperone from Escherichia coli" Biopolymers, 2010, 93, 47-60.
  19. Lewandowska, A., Ołdziej, S., Liwo, A., Scheraga, H.A. "Mechansm of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. Part III. Dynamics of long-range hydrophobic interactions. Proteins: Struct. Funct. and Bioinf., 2010, 78, 723-737.
  20. Lewandowska, A., Ołdziej, S., Liwo, A., Scheraga, H.A. "Mechanism of formation of the C-terminal B-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. Part IV. Implication for the mechanism of folding of the parent protein." Biopolymers, 2010, 93, 469-480.
  21. Lewandowska, A., Ołdziej, S., Liwo, A., Scheraga, H.A. "ß-hairpin-forming peptides; models of early stages of protein folding." Biophys. Chem., 2010, 151, 1-9.

2009

  1. Ciarkowski, J., Czaplewski, C., Łuczak, S., Rodziewicz-Motowidło, S., Schiller, P.W. Conformation-activity relationships of cyclo-constrained mu-delta opioid agonists derived from the N-terminal tetrapeptide segment of dermorphin/deltorphin, in Advances in Experimental Medicine and Biology, Editors: S. DelValle, E. Escher, W.D. Lubell; The Proceedings of the 20th American Peptide Symposium, Montreal, June 26-30 2007, 2009, 489-490.
  2. Liepina, I., Ventura, S., Czaplewski, C., Liwo, A. "Dynamics study on single and multiple beta-sheets, in Advances in Experimental Medicine and Biology, Editors: S. DelValle, E. Escher, W.D. Lubell; The Proceedings of the 20th American Peptide Symposium, Montreal, June 26-30 2007, 2009, 293-294.
  3. Ciarkowski, J., Zieleniak, A., Rodziewicz-Motowidło, S., Rusak, Ł., Chung, N.N., Czaplewski, C., Witkowska, E., Schiller P.W., Izdebski, J. "Deltorphin analogs restricted via a urea bridge: structure and opioid activity", in Advances in Experimental Medicine and Biology, Editors: S. DelValle, E. Escher, W.D. Lubell; The Proceedings of the 20th American Peptide Symposium, Montreal, June 26-30 2007, 2009, 491-492.
  4. Czaplewski, C., Kalinowski, S., Liwo, A., Scheraga, H.A. "Application of multiplexed replica exchange molecular dynamics to the UNRES force field: tests with alpha and alpha+beta proteins" J. Chem. Theor. Comput., 2009, 5, 627-640.
  5. Maisuradze, G.G., Liwo, A., Scheraga, H.A, "Principal component analysis for protein folding dynamics" J. Mol. Biol., 2009, 385, 312-329.
  6. Rodziewicz-Motowidło, S., Iwaszkiewicz, J., Sosnowska, R., Czaplewska, P., Sobolewski, E., Szymanska, A., Stachowiak, K., Liwo, A. "The role of the Val57 amino-acid residue in the hinge loop of the human cystatin C. Conformational studies of the beta2-L1-beta3 segments of wild type human cystatin C and its mutants" Biopolymers, 2009, 91, 373-383.
  7. Ślusarz, R., Ślusarz, M.J. "An Influence of the Aromatic Side Chains Conformations in Positions 2 and 3 of Vasopressin Analogs on Interaction with Vasopressin and Oxytocin Receptors" QSAR Comb. Sci., 2009, i28, 1166-1175.
  8. Skwierawska, A., Makowska, J., Ołdziej, S., Liwo, A., Scheraga, H.A. "Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure. Proteins: Strut. Funct. Bioinfo., 2009, 75, 931-953.
  9. Ślusarz, M.J., Ślusarz, R., Ciarkowski, J. "Molecular dynamics study of the internal water molecules in vasopressin and oxytocin receptors" Protein Pept. Lett., 2009, 16, 342-350.
  10. Skwierawska, A., Żmudzinska, W., Ołdziej, S., Liwo, A., Scheraga, H.A. "Mechanism of formation of the C-terminal beta-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: Strut. Funct. Bioinfo., 2009, 76, 637-654. ,
  11. Sobiecka-Szkatula, A., Polit, A., Scire, A., Giełdoń, A., Tanfani, F., Szkarlat, Z., Ciarkowski, J., Zurawa-Janicka, D., Skorko-Glonek, J., Lipinska, B. "Temperature-induced conformational changes within the regulatory loops L1-L2-LA of the HtrA heat-shock protease from Escherichia coli" BBA, 2009, 1794, 1573-1582.
  12. Shen, H., Liwo, A., Scherega, H.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" J. Phys. Chem. B, 2009, 113, 8738-8744.
  13. Maisuradze, G.G., Liwo, A., Scheraga, H.A. "How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?" Phys. Rev. Lett., 2009, 102, 238102.
  14. He, Y., Xiao, Y., Liwo, A., Scheraga, H.A. "Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field" J. Comput. Chem., 2009, 30, 2127-2135.
  15. Sobolewski, E., Makowski, M., Ołdziej, S., Czaplewski, C., Liwo, A., Scheraga, H.A. 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. PEDS, 2009, 22, 547-552.

2008

  1. Liwo, A., Czaplewski, C., Ołdziej, S., Rojas, S.V., Kaźmierkiewicz, R., Makowski, M., Murarka R.K., Scheraga, H.A. Chapter 8. "Simulation of protein structure and dynamics with the coarse-grained UNRES force field", in Coarse-Graining of Condensed Phase and Biomolecular Systems, edited by G.A. Voth, CRC Press Taylor and Francis Group, 2008, 107-122.
  2. Skwierawska, A., Rodziewicz-Motowidło, S. Ołdziej, S., Liwo, A., H.A. Scheraga. "Conformational studies of the α-helical 28-43 fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus" Biopolymers: Peptide Science", 2008, 89, 1032-1044.
  3. Makowska, J., Bagińska, K., Liwo, A., Chmurzyński, L., Scheraga, H.A "Acidic-basic properties of three alanine-based peptides containing acidic and basic side chains: Comparison between theory and experiment" Biopolymers: Peptide Science, 2008, 90, 5, 724-732.
  4. Ossowski, T., Goulart, M.OF., de Abreu, F.C., Sant'Ana A.E.G., Zarzeczanska, D., Miranda, P.R.B., Costa, D.C., Liwo, A., Falkowski., P. "Determination of the pKa values of some biologically active and inactive hydroxyquinones" J. Braz. Chem. Soc., 2008, 19, 175-183.
  5. Liwo, A., Czaplewski, C., Ołdziej, S., Scheraga, H.A. "Computational techniques for efficient conformational sampling of protein" Curr. Opinion Struct. Biol. 2008, 18, 134-139.
  6. Kleinerman, D.S., Czaplewski, C., Liwo, A., Scheraga, H.A. "Implementations of Nose-Hoover and Nose-Poincare thermostats in mesoscopic dynamic simulations with the united-residue" J. Chem. Phys., 2008 128, 245103.
  7. Shen, H., Czaplewski, C., Liwo, A., Scheraga, H.A. "Implementation of a Serial Replica Exchange Method in a physics-based united-residue (UNRES) force field" J. Chem. Theor. Comput, 2008, 4, 1386-1400.
  8. Makowski, M., Sobolewski, E., Czaplewski, C., Ołdziej, S., Liwo, A., Scheraga, H.A. "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" J. Phys. Chem. B, 2008, 112, 11385-11395.
  9. Rodziewicz-Motowidło, S., Czaplewski, C., Łuczak, S., Ciarkowski, J. "Conformation-activity relationships of cyclo-constrained μ/δ opioid agonists derived from the N-terminal tetrapeptide segment of dermorphin/deltorphin" J. Pept. Sci., 2008, 14, 898-902.
  10. Ślusarz, R., Sikorska, E., Ślusarz, M.J. "Theoretical study on interactions of bicyclic vasopressin analogues with human neurohypophyseal hormone receptors" QSAR Comb. Sci., 2008, 27, 834-840.
  11. Zieleniak, A., Rodziewicz-Motowidło, S., Rusak, Ł., Chung, N.N., Czaplewski, C., Witkowska, E., Schiller, P.W., Ciarkowski, J., Izdebski, J. "Deltorphin analogs restricted via a urea bridge: structure and opioid activity" J. Pept. Sci., 2008, 14, 830-837.
  12. Witt, M., Ślusarz, M.J., Ciarkowski, J. "Molecular Modeling of Vasopressin V2 Receptor Tetramer in Hydrated Lipid Membrane" QSAR Comb. Sci., 2008, 27, 684-693.
  13. Seo, M., Castillo, N., Ganzynkowicz, R., Daniels, C.R., Woods, R.J., Lowary, T.L., Roy, P-N. "Approach for the Simulation and Modeling of Flexible Rings: Application to the α-D-Arabinofuranoside Ring, a Key Constituent of Polysaccharides from Mycobacterium tuberculosis", J. Chem. Theory Comput., 2008, 4, 184-191.

2007

  1. Sobolewski, E., Makowski, M., Czaplewski, C., Liwo, A., Ołdziej, S., Scheraga, H.A. "Potential of mean force of hydrophobic association: Dependence on solute size" J. Phys. Chem. B, 2007, 111, 10765-10774.
  2. Witt, M., Ciarkowski, J., Czaplewski, C., "Molecular Simulations of Rhodopsin Tetrameter" Prot. Pept. Lett., 2007, 14, 381-387.
  3. Wieczerzak, E., Rodziewicz-Motowidło, S., Jankowska, E., Giełdoń, A., Ciarkowski, J. "An enormously active and selective azapeptide inhibitor of cathepsin B" J. Pept. Sci., 2007 13, 536-543.
  4. Kozłowska, U., Liwo, A., Scheraga, H.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" J. Phys-Cond Mat, 2007, 19, No. 285203.
  5. Chinchio, M., Czaplewski, C., Liwo, A., et al. "Dynamic formation and breaking of disulfide bonds in molecular dynamics simulations with the UNRES force field" J. Chem. Theor. Comput., 2007, 3, 1236-1248.
  6. Niv. M.Y., Ripoll, D.R., Vila, J.A., Liwo, A., Vanamee, E.S., Aggarwal, A.K., Weinstein, H., Scheraga H.A. "Topology of type II REases revisited; structural classes and the common conserved core" Nucl. Acids Res. 2007, 35, 2227-2237.
  7. Grajek, H., Liwo, A., Wiczk, W., Żurkowska, G. "Resolution of the excitation-emission spectra of FMN in rigid poly(vinyl alcohol) matrices" J. Photochem. Photobiol. B , 2007, 86, 193-198.
  8. Makowski, M., Sobolewski, E., Czaplewski, C., Liwo, A., Ołdziej, S., No, J.H., Scheraga, H.A. "Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 3. Calculation and parameterization of the potentials of mean force of pairs of identical hydrophobic side chains" J Phys Chem B. 2007 111, 2925-2931.
  9. Makowski, M., Liwo, A., Maksimiak, K., Makowska, J., Scheraga, H.A. "Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 2. Tests with simple spherical systems. J Phys Chem B. 2007, 111, 2917-2924.
  10. Makowski, M., Liwo, A., Scheraga, H.A. "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." J Phys Chem B. 2007, 111, 2910-2916.
  11. Bobrowski, M., Liwo, A., Hirao, K. "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" J Phys Chem B., 2007, 111, 3543-3549.
  12. Makowska, J., Rodziewicz-Motowidło, S., Bagińska, K., Vila, J.A., Liwo, A., Chmurzyński, L., Scheraga, H.A. "Further Evidence for the Absence of Polyproline II Stretch in the XAO Peptide" Biophys. J., 2007, 92, 2904-2917.
  13. Scheraga, H.A., Khalili, M., Liwo, A. "Protein-folding dynamics: Overview of molecular simulation techniques" Annu. Rev. Phys. Chem., 2007, 58, 57-83.
  14. Rojas, A.V., Liwo, A., Scheraga, H.A. "Molecular dynamics with the united-residue force field: Ab Initio folding simulations of multichain proteins" J. Phys. Chem. B., 2007, 111, 293-309.
  15. Liwo, A., Khalili, M., Czaplewski, C., Kalinowski, S., Ołdziej, S., Wachucik, K., Scheraga, H.A. "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." J. Phys. Chem. B, 2007, 111, 260-285.
  16. Piotrowska, E., Rodziewicz-Motowidło, S., Wieczerzak, E., Grzonka, Z., Ciarkowski, J. "Comparative conformational studies of Z-RLR(aza)GIV-OMe - the potent and selective Cathepsin B inhibitor and Z-RLRGIV-OMe - its parent peptide" Peptides 2006, eds. K.Rolka, P.Rekowski, J.Silberring, Kenes International, 2007, 418-419.
  17. Ślusarz, M.J., Ślusarz, R., Ciarkowski, J. "Vasopressin and oxytocin receptors interactions with agonists and antagonists - molecular modeling study" Peptides 2006, eds. K.Rolka, P.Rekowski, J.Silberring, Kenes International, 2007, 366-367.
  18. Ślusarz, R., Ślusarz, M.J., Lammek, B. "Molecular modeling-based study of new vasopressin analogs affinity toward human neurohypophyseal hormone receptors",Peptides 2006, eds. K.Rolka, P.Rekowski, J.Silberring, Kenes International, 2007, 396-397.
  19. Mickiewicz, B., Kamysz, B., Greber, K., Rodziewicz-Motowidło, S. "Conformational Studies of Antimicrobial Protegrin-1 Analogues, BM-1 and BM-2, by using NMR Spectroscopy" Peptides 2006, eds. K.Rolka, P.Rekowski, J.Silberring, Kenes International, 2007, 532-533.
  20. Rodziewicz-Motowidło, S., Skwierawska, A., Ołdziej, S., Wiczk, W., Liwo, A., Scheraga, H.A. "Conformational studies of a short peptide corresponding to the C-terminal β-hairpin structure of the B1 domain of protein G" Peptides 2006, eds. K.Rolka, P.Rekowski, J.Silberring, Kenes International, 2007,

2006

  1. Rakowski, F., Grochowski, P., Lesyng, B., Liwo, A., Scheraga, H.A. "Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united residue mesoscopic potential energy function" J. Chem. Phys., 2006 125, 204107.
  2. Liepina, I., Ventura, S., Czaplewski, C., Liwo, A. "Molecular dynamics study of amyloid formation of two Abl-SH3 domain peptides" J. Pept. Sci., 2006, 780-789.
  3. Khalili, M., Liwo, A., Scheraga, H.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" J. Mol. Biol. , 2006, 355, 536-547.
  4. Ślusarz, M.J., Sikorska, E., Ślusarz, R., Ciarkowski, J. "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" J. Med. Chem., 2006, 49, 2463-2469.
  5. Makowska, J., Makowski, M., Jagielska, A., Liwo, A., Kasprzykowski, F., Chmurzyński, L., Scheraga, H.A. "Assessment of two teoretical methods to estimate potentiometric titration curves of peptides: comparison with experiment" J. Phys. Chem. B, 2006, 110, 4451-4458.
  6. Sikorska, E. Ślusarz, M.J., Lammek, B. "Conformational studies of AVP analogues modified with N-methylphenylalanine enantiomers in dimethyl sulfoxide solution" Biopolymers, 2006, 82, 603-614.
  7. Ślusarz, M.J., Ślusarz, R., Ciarkowski, J. "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, 81, 321-338.
  8. Makowska, J., Rodziewicz-Motowidło, S., Baginska, K., Vila, J.A., Liwo, A., Chmurzynski, L., Scheraga, H.A. "Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins", PNAS, 2006, 103, 1744-1749.
  9. Ślusarz, M.J., Ślusarz, R., Ciarkowski, J. "Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin - modeling of an activated state." J. Pept. Sci., 2006, 12, 171-179.
  10. Ślusarz, M.J., Giełdoń, A., Ślusarz, R., Ciarkowski, J. "Analysis of interactions responsible for vasopressin binding to human neurohypophyseal hormone receptors - molecular dynamics study of the activated receptor-vasopressin-Gα systems." J. Pept. Sci., 2006, 12, 180-189.
  11. Ślusarz, R., Ślusarz, M.J., Lammek, B., Ciarkowski, J. "Molecular Modeling of MetaII rhodopsin." QSAR Comb. Sci., 2006, 25, 105-113.
  12. Sikorska, E., Ślusarz, M.J., Ślusarz R., Lammek B. "Investigation of cis/trans ratios of peptide bonds in AVP analogues containing N-methylphenylalanine enantiomers", J. Pept. Sci., 2006, 12, 13-24.
  13. Ciarkowski, J., Drabik, P., Grzonka, Z., Hruby, V., Liwo, A., Ołdziej, S., Politowska, E., Shenderovich M.D., Witt, M. "From modeling neurohypophyseal hormones to signaling mechanisms in GPCRs." Peptides 2004, M.Flegel, M.Fridkin, C.Gilon, J.Slaninowa, Kenes International, 2006, 125-128. i
  14. Łągiewka, J., Rodziewicz-Motowidło, S., Sosnowska, R., Stachowiak, K., Ołdziej, S., Liwo, A., Grzonka, Z. "Investigation of the hCC dimerization mechanism . CD and NMR structural stability studies of the beta-2-L1-beta-3 fragment", Peptides 2004, M.Flegel, M.Fridkin, C.Gilon, J.Slaninowa, Kenes International, 2006, 1029-1030.

2005

  1. Ślusarz, M.J., Ciarkowski, J. "Receptory sprzężone z białkiem G - model z wyboru Natury do projektowania leków in silico", W: "Na pograniczu chemii i biologii, tom XII", Wydawnictwo Naukowe Uniwersytetu Adama Mickiewicza w Poznaniu, Poznań 2005, 169-192.
  2. Ciarkowski, J., Witt, M., Ślusarz, R. "A hypothesis for GPCR activation." J. Mol. Mod. , 2005, 11, 407-415.
  3. Ślusarz, M.J., Giełdoń A., Ślusarz, R., Meadows, R., Trojnar, R., Ciarkowski, J. "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 Comb. Sci., 2005, 24, 603-610.
  4. Makowska, J., Bagińska, K., Kasprzykowski, F., Vila, J.A., Jagielska, A., Liwo, A., Chmurzyński, L., Scheraga, H.A., "Interplay of charge distribution and conformation for peptides: comparison of theory and experiment." Biopolymers, 2005, 80, 214-224.
  5. Makowska, J., Makowski, M., Liwo, A., Chmurzyński L."Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid base interactions in side chains of biomolecules using the potenti al of mean force." J. Comput. Chem., 2005, 235-242.
  6. Liwo, A., Khalili, M., Scheraga, H.A. "Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains." Proc. Natl. Acad. Sci. U.S.A., 2005, 102, 2362-2367
  7. Czaplewski, C., Liwo, A., Ripoll, D.R., Scheraga, H.A. "Molecular origin of anticooperativity in hydrophobic association." J. Phys. Chem., 2005, 109, 8108-8119.
  8. Ołdziej, S., Czaplewski, C., Liwo, A., Chinchio, M., Nanias, M., Vila, J.A., Khalili, M., Arnautova, Y.A., Jagielska, A., Makowski, M., Schafroth, H.D., Kaźmierkiewicz, R., Ripoll, D.R., Pillardy, J., Saunders, J.A., Kang, Y.K., Gibson, K.D., Scheraga, H.A. "Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests." Proc. Natl. Acad. Sci. U.S.A., 2005, 102, 7547-7552.
  9. Khalili, M., Liwo, A., Rakowski, F., Grochowski, P., Scheraga, H.A. "Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode." J. Phys. Chem. B, 2005, 109, 13785-13797.
  10. Khalili, M., Liwo, A., Jagielska, A., Scheraga, H.A. "Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model α-helical systems. J. Phys. Chem. B, 2005, 109, 13798-13810.
  11. Liepina, I., Janmey, P.A., Czaplewski, C., Liwo, A., "Membrane initiated gelsolin amyloid formation." Biopolymers, 2005, 80, 596-597.
  12. Czaplewski, C., Kalinowski, S., Liwo, A., Scheraga, H.A. "Comparison of two approaches to potential of mean force calculations of hydrophobic association: particle insertion and weighted histogram analysis methods." Mol. Phys., 2005, 103, 3153-3167.
  13. Czaplewski, C., Kalinowski, S., Liwo, A., Ripoll, D.R., Scheraga, H.A. "Comment on 'Molecular origin of anticooperativity in hydrophobic association", J. Phys. Chem. B, 2005, 21222-21224

2004

  1. Makowska, J., Makowski, M., Giełdoń, A., Liwo, A., Chmurzyński, L. "Theoretical calculations of heteroconjugation equilibrium constants in systems sodeling acid-base interactions in side chains of biomolecules using the potential of mean force", J. Phys. Chem. B., 2004, 32, 12222-12230.
  2. Malicka, J., Czaplewski, C., Groth, M., Wiczk, W., Ołdziej, S., Łankiewicz, L., Ciarkowski, J., Liwo, A. "Use of NMR spectroscopy as well as theoretical conformational analysis in Conformation-activity studies of cyclic enkephalin analogues." Current Topics Med. Chem., 2004, 4, 123-133.
  3. Ślusarz, R., Ciarkowski, J. "Interaction of class A G protein-coupled receptors with G proteins" Acta Biochim. Polon., 2004, 51, 129-136.
  4. Ślusarz, M.J., Ślusarz, R., Meadows, R., Trojnar, R. and Ciarkowski, J. "Molecular dynamics of complexes of atosiban with neurohypophyseal receptors in the fully hydrated phospolipid bilayer." QSAR Comb. Sci., 2004, 23,536-545.
  5. Liwo, A., Ołdziej, S., Czaplewski, C., Kozłowska, U., Scheraga, H.A. "Parametrization of backbone-electrostatic and multibody contributions to the UNRES force field for protein-structure prediction from ab initio energy surfaces of model systems." J. Phys. Chem. B, 2004, 108, 9421-9438
  6. Czaplewski, C., Ołdziej, S., Liwo, A., Scheraga, H.A. "Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds." Prot. Eng. Des. Select., 2004, 17, 29-36.
  7. Czaplewski, C., Liwo, A., Pillardy, J., Ołdziej, S., Scheraga, H.A. "Improved conformational space annealing method to treat beta-structure with the UNRES force-field and to enhance scalability of parallel implementation." Polymer, 2004, 45, 677-686.
  8. Khalili, M., Saunders, J.A., Liwo, A., Ołdziej, S., Scheraga, H.A. "A united residue force-filed for calcium-protein interactions." Prot. Sci., 2004, 13, 2725-2735.
  9. Liwo, A., Arłukowicz, P., Ołdziej, S., Czaplewski, C., Makowski, M., Scheraga, H.A. "Optimization of the UNRES froce filed by hierarchical design of the potential-energy landscape. 1.Tests of the approach using simple lattice protein models." J. Phys. Chem. B, 2004, 108, 16918-16933.
  10. Ołdziej, S., Liwo, A., Czaplewski, C., Pillardy, J., Scheraga, H.A. "Optimization of the UNRES froce filed by hierarchical design of the potential-energy landscape. 2. Off-lattice tests of the method with single protein." J.Phys.Chem. B, 2004, 108, 16934-16949.
  11. Ołdziej, S., Łągiewka, J., Liwo, A., Czaplewski, C., Chinchio, M., Nanias, M., Scheraga, H.A. "Optimization of the UNRES froce filed by hierarchical design of the potential-energy landscape. 3. Use many proteins in optimization." J. Phys. Chem. B, 2004, 108, 16950-16959.
  12. Guzow, K., Ganzynkowicz, R., Rzeska, A., Mrozek, J., Szabelski, M., Karolczak, J., Liwo, A., Wiczk, W. "Photophysical properties of tyrosine and its simple derivatives studied by time-resolved fluorescence spectroscopy, global analysis and theoretical calculations" J. Phys. Chem. B, 2004, 108, 3879-3889.

2003

  1. Giełdoń, A., Kaźmierkiewicz, R., Ślusarz, R., Pasenkiewicz-Gierula, M., Ciarkowski, J. "Molecular dynamics study of Phenylacetyl-d-Y(Et)FQNKPR-NH2 selectivity to V1a receptor." J. Mol. Mod., 2003, 9, 372-378.
  2. Ślusarz, M.J., Ślusarz, R., Kaźmierkiewicz, R., Trojnar, J.,Wiśniewski K., Ciarkowski, J. "Molecular modeling of the neurohypophyseal receptor/atosiban complexes." Protein Pept. Lett., 2003, 3, 295-302.
  3. Giełdoń, A., Ciarkowski, J. "Modeling interactions of oxytocin and vasopressin receptors with selected antagonists." Ann Polish Chem Soc., 2003, 93-96.
  4. Ślusarz, R., Ślusarz, M.J., Kaźmierkiewicz, R., Lammek, B. "Molecular modeling of interaction of the vasopressin analogs with vasopressin and oxytocin receptors." QSAR Comb. Sci., 2003, 22, 865-872.
  5. Ołdziej, S., Kozłowska, U., Liwo, A., Scheraga, H.A. "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, J. Phys. Chem. A, 2003, 107, 8035-8046.
  6. Czaplewski, C., Rodziewicz-Motowidło, S., Dąbal, M., Liwo, A., Ripoll, D.R., Scheraga, H.A. "Molecular Simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles", Special Kauzmann Issue of Biophysical Chemistry, 2003, 105, 339-359.
  7. Maksimiak, K., Rodziewicz-Motowidło, S., Czaplewski, C., Liwo, A., Scheraga, H.A. "Molecular Simulation Study of the Potentials of Mean Force for the Potentials of Mean Force for the Interactions Between Models of Like-Charged as well as Between Charged and Nonpolar Amino-Acid Side Chains in Water", J. Phys. Chem. B, 2003, 107, 13496-13504.
  8. Guzow, K., Mazurkiewicz, K., Szabelski, M., Ganzynkowicz, R., Karolczak, J., Wiczk, W. "Influence of an aromatic substituent in position 2 on photophysical properties of benzoxazol-5-yl-alanine derivatives", Chem. Phys., 2003, 295, 119-130.

2002

  1. Politowska, E., Drabik, P., Kaźmierkiewicz, R., Ciarkowski, J. "Docking ligands to vasopressin and oxytocin receptors via genetic algorithm." J Sign. Transd. Rec. Res., 2002, 22, 395-411.
  2. Rodziewicz-Motowidło, S., Zhukov, I., Kasprzykowski, F., Grzonka, Z., Ciarkowski, J., Wójcik, J. "Conformational solution studies of [Sar7]desamino- and [MeAla7]desamino-vasopressin analogues using NMR spectroscopy." J. Pept. Sci. 2002, 8, 347-364.
  3. Czaplewski, C., Ripoll, D.R., Liwo, A., Rodziewicz-Motowidło, S., Wawak, R.J., Scheraga, H.A. "Can cooperativity in hydrophobic association be reproduced correctly by implicit solvation models." IJQC, 2002, 88, 41-55.
  4. Liwo, A., Arłukowicz, P., Czaplewski, C., Ołdziej, S., Pillardy, J., Scheraga, H.A. "A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field." PNAS, 2002,99, 1937-1942.
  5. Malicka, J., Groth, M., Czaplewski, C., Wiczk, W., Liwo, A. "Conformational studies of cyclic enkephalin, analogues with L- or D-proline in position 3." Biopolymers, 2002, 63, 217-231.
  6. Scheraga, HA., Pillardy, J., Liwo, A., Lee, J., Czaplewski, C., Ripoll, D.R., Wedemeyer, W.J., Arnautova, Y.A. "Evolution of physics-based methodology for exploring the conformational energy landscape of proteins." J. Comp. Chem., 2002, 23, 28-34.

2001

  1. Malicka, J., Ganzynkowicz, R., Groth, M., Czaplewski, C., Karolczak, J., Liwo, A., Wiczk, W. "Fluorescence decay time distribution analysis of cyclic enkephalin analogues; influence of solvent and Leu configuration in position 5 on conformation", Acta Biochim. Polon., 2001, 48, 95-102.
  2. Ganzynkowicz R., Liwo A., Wiczk W. "A fluorescence, 1H NMR spectroscopy and molecular dynamics study of the influence of rotamer population on fluorescence decay of tyrosine, phenylalanine and their derivatives", TASK Quarterly, 2001, 5, 311-316.
  3. Ganzynkowicz, R., Rzeska, A., Liwo, A., Wiczk, W. "3. Influence of a rotamer population on fluorescence decay of the tyrosine derivatives studied by fluorescence, 1H NMR spectroscopy and theoretical calculations" in Peptides 2000, Peptides 2000, J. Martinez and J.-A. Fehrenz, Eds, EDK, Paris, 2001, 411-412.
  4. Drabik, P., Liwo, A., Czaplewski, C., Ciarkowski, J. "The investigation of the effects of counterions in protein dynamics simulation." Protein Eng., 2001, 14, 747-752.
  5. Ślusarz,R., Kaźmierkiewicz, R., Giełdoń, A., Ciarkowski, J. "Molecular docking-based test for affinities of two ligands toward vasopressin and oxytocin receptors." Acta Biochim. Polon., 2001, 48, 131-135.
  6. Politowska, E., Kaźmierkiewicz, R., Wiegand, V., Fahrenholz F., Ciarkowski, J. "Molecular modelling study on a role of cholesterol in the stimulation of the oxytocin receptor." Acta Biochim. Polon., 2001, 48, 83-93.
  7. Woźniak-Celmer, E., Ołdziej, S., Ciarkowski, J. "Theoretical models of catalytic domains of protein phosphatases 1 and 2a with Zn+2 and Mn+2 metal dications and putative bioligands in their catalytic centers." Acta Biochim. Polon., 2001, 48, 35-52.
  8. Grzonka, Z., Jankowska, E., Kasprzykowski, F., Kasprzykowska, R., Łankiewicz, L., Wiczk, W., Wieczerzak, E., Ciarkowski, J., Drabik, P., Janowski, R., Kozak, M., Jaskólski, M., Grubb, A. "Structural studies of cysteine proteases and their inhibitors." Acta Biochim. Polon., 2001, 48, 1-20, REVIEW.
  9. Woźniak-Celmer, E., Ołdziej, S., Ciarkowski, J. "Ser/Thr protein phosphatase-1 and -2A catalytic units: simulation of their interactions with selected substrate and inhibitor sequences." Cell. Mol. Biol. Lett., 2001, 6, 554-556.
  10. Ciarkowski, J., Drabik, P., Giełdoń, A., Kaźmierkiewicz, R., Ślusarz, R. "Signal transmission via G protein-coupled receptors (GPCRs) in view of the rhodopsin structure determination." Acta Biochim. Polon., 2001, 48, 1203-1207.
  11. Giełdoń, A., Kaźmierkiewicz, R., Ślusarz, R., Ciarkowski, J. "Molecular modeling of interactions of the non-peptide antagonist YM087 with the human vasopressin V1a, V2 receptors and with oxytocin receptor." JCAMD, 2001, 15, 1085-1104.
  12. Ciarkowski, J., Drabik, P., Giełdoń, A., Kaźmierkiewicz, R., Ślusarz, R. "Neurophyseal receptors-ligands: where we are after the landmark rhodopsin structure structure determination." Peptides 2001 (Proc 17th APS), 2001, M.Lebl & R.A.Houghten, Eds. American Peptide Society, 896-897.
  13. Czaplewski, C., Rodziewicz-Motowidło, S., Liwo, A., Ripoll, D.R., Wawak, R.J., Scheraga, H.A. "Comment on "Anti-cooperativity" in hydrophobic interactions: A simulation study of spatial dependence of three-body effects and beyond." J. Chem. Phys., 2001, 115, 1414-1421.
  14. Groth, M., Malicka, J., Rodziewicz-Motowidło, S., Czaplewski, C., Klaudel, L., Wiczk, W., Liwo, A. "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, 60, 79-95.
  15. Pillardy, J., Czaplewski, C., Liwo, A., Wedemeyer, W.J., Lee, J., Ripoll, D.R., Arłukowicz, P., Ołdziej, S., Arnautova, Y.A., Scheraga, H.A. " Development of physics-based energy functions that predict medium-resolution structures for proteins of the alpha,beta and alpha/beta structural classes." J. Phys. Chem. B, 2001, 105, 7299-7311.
  16. Liwo, A., Czaplewski, C., Pillardy, J., Scheraga, H,A. "Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field." J. Chem. Phys., 2001, 115, 2323-2347.
  17. Pillardy, A., Czaplewski, C., Liwo, A., Lee, J., Ripoll, D.R., Kaźmierkiewicz, R., Ołdziej, S., Wedemeyer, W.J., Gibson, K.D., Arnautova, Y.A., Saunders, J., Ye, Y.J., Scheraga, H.A. "Recent improvements in prediction of protein structure by global optimization of a potential energy function." PNAS, 2001, 98, 2329-2333.
  18. Malicka, J., Groth, M., Karolczak, J., Czaplewski, C., Liwo, A., Wiczk, W. "Influence of solvents and leucine configuration at position 5 on tryptophan fluorescence in cyclic enkephalin analogues." Biopolymers, 2001, 58, 447-457.
  19. Rodziewicz-Motowidło, S., Lesner, A., Rolka, K., Łęgowska, A., Czaplewski, C., Liwo, A., Patacchni, R., Quartara, L. "Conformational Studies of Scyliorhinin II Analogues - Tachykinin Peptides, Using NMR Spectroscopy and Global Monte Carlo Analysis", J. Pept. Research, 2001, 58, 159-172. 
Treść ostatnio zmodyfikowana przez: Magdalena Ślusarz
Treść wprowadzona przez: Magdalena Ślusarz
Ostatnia modyfikacja: 
wtorek, 27 listopada 2018 roku, 11:22