Publikacje Naukowe | Wydział Chemii

Publikacje naukowe

Use of Coarse-Grained and All-Atom Molecular Dynamics to Study Hsp70 and Hsp40 Chaperone Action,
E.I. Golas, M.A. Mozolewska, P. Krupa, C. Czaplewski, H.A. Scheraga, A. Liwo
in Frontiers in Structural Biology Vol. 1 edited by M.D. Galigniana, Bentham Publishers, pp 23-46 (2018).
ISBN: 978-1-68108-616-3

High performance computing with coarse-grained model of biological macromolecules,
E. Lubecka, A. Sieradzan, C. Czaplewski, P. Krupa, A. Liwo,
Supercomputing Frontiers and Innovations 2018, 5, 63-75.

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,
M. J. Grzeszczuk, A. Bak, A. M. Banas, P. Urbanowicz, S. Dunin-Horkawicz, A. Gieldon, C. Czaplewski, A. Liwo, E.K. Jagusztyn-Krynicka,
Plos One 2018, 13, e0195358.

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics,
C. Czaplewski, A. Karczyńska, A.K Sieradzan, A. Liwo
Nucleic Acids Res. 2018, 46, W304-W309.

Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: test with CASP12 targets,
A. Karczyńska, M.A. Mozolewska, P. Krupa, A.Giełdoń, K.K. Bojarski, B. Zaborowski, A. Liwo, R. Ślusarz, M. Ślusarz, J. Lee, K. Joo, C. Czaplewski,
J. Mol. Graph. Model. 2018, 83, 92-99.

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12,
C. Keasar, L. McGuffin, B. Wallner, G. Chopra, B. Adhikari, D. Bhattacharya, L. Blake, L. Bortot, R. Cao, B.K. Dhanasekaran, I. Dimas, R. Faccioli, E. Faraggi, R. Ganzynkowicz, S. Ghosh, S. Ghosh, A. Gieldon, L. Golon, Y. He, L. Heo, J. Hou, M. Khan, F. Khatib, G. Khoury, C. Kieslich, D. Kim, P. Krupa, G.R. Lee, H. Li, J. Li, A. Lipska, A. Liwo, A. Maghrabi, M. Mirdita, S. Mirzaei, M. Mozolewska, M. Onel, S. Ovchinnikov, A. Shah, U. Shah, T. Sidi, A. Sieradzan, M. Ślusarz, R. Slusarz, J. Smadbeck, P. Tamamis, N. Trieber, T. Wirecki, Y. Yin, Y. Zhang, J. Bacardit, M. Baranowski, N. Chapman, S. Cooper, Al. Defelicibus, J. Flatten, B. Koepnick, Z. Popović, B. Zaborowski, D. Baker, J. Cheng, C. Czaplewski, A. Delbem, C. Floudas, A. Kloczkowski, S. Ołdziej, M. Levitt, H. Scheraga, C. Seok, J. Söding, S. Vishveshwara, D. Xu, and S. Crivelli
Scientific Reports 2018, 8, 9939.

Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information,
A. Karczyńska, M.A. Mozolewska, P. Krupa, A. Giełdoń, A. Liwo, C. Czaplewski,
Proteins: Struct. Funct. Bioinf. 2018, 86, 228-239. CASP12 special issue.

Acid-base properties of 3-[2-(n-quinolinyl)benzoxazol-5-yl]alanine derivatives in the ground and excited state. Experimental and theoretical studies,
A. Lewandowska, D. Wroblewski, K. Guzow, M. Milewska, C. Czaplewski, W. Wiczk
J. Photochem. Photobiol. A - Chemistry 2018, 353, 191-199.

Biochemical properties of the HtrA homolog from bacterium Stenotrophomonas maltophilia,
U. Zarzecka, A. Modrak-Wojcik, M. Bayassi, M. Szewczyk, A. Gieldon, A. Lesner, T. Koper, A. Bzowska, M. Sanguinetti, S. Backert, B. Lipinska, J. Skorko-Glonek,
Int. J. Biol. Macromol. 2018, 109, 992-1005.

Microscopic Physics-Based Models of Proteins and Nucleic Acids: UNRES and NARES,
M. Baranowski, C. Czaplewski, E. Golas, Y. He, D. Jagiela, P. Krupa, A. Liwo, G.G. Maisuradze, M. Makowski, M.A. Mozolewska, A. Niadzvedtski, A.J. Niemi, S. Rackovsky, R. Slusarz, A.K. Sieradzan, S. Oldziej, T. Wirecki, Y. Yin, B. Zaborowski, H.A. Scheraga,
in Coarse-Grained Modeling of Biomolecules (Series in Computational Biophysics), edited by G.A. Papoian, CRC Press (2018) pp. 67-120.
ISBN 978-1-4665-7606-3

Chemoinformatics methods for studying biomolecules,
A. Liwo, C. Czaplewski, S. Ołdziej, B. Zaborowski, D. Jagieła, J. Lee,
in Handbook of computational chemistry, edited by J. Leszczyński. Springer (2017) pp. 2183-2199.
ISBN 978-3-319-27281-8

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins,
A. Karczyńska, C. Czaplewski, P. Krupa, M. Mozolewska, K. Joo, J. Lee, A. Liwo,
J. Comput. Chem. 2017, 38, 2730–2746.

Crystal structure of a low molecular weight activator Blm-pep with yeast 20S proteasome – insights into the enzyme activation mechanism,
J. Witkowska, M. Giżyńska, P. Grudnik, P. Golik, P. Karpowicz, A. Giełdoń, G. Dubin, E. Jankowska,
Sci. Rep. 2017, 7, 6177.

Rapid insight into C60 influence on biological functions of protein,
A. Giełdoń, M. Witt, A. Gajewicz, T. Puzyn,
Struct. Chem. 2017, 28, 1775-1788.

Selection of effective HTRA3 activators using combinatorial chemistry,
M. Wysocka, K. Sychowska, N. Gruba, Ł. Winiarski, M. Skoreński, M. Psurski, J. Makowska, A. Giełdoń, T. Wenta, M. Jarząb, P. Glaza, J. Zdancewicz, M. Sieńczyk, B. Lipińska, A. Lesner.,
ACS Comb. Sci. 2017, 19, 565-573.

Structural insights into the activation mechanisms of human HtrA serine proteases,
D. Żurawa-Janicka, T. Wenta, M. Jarząb, J. Skórko-Glonek, P. Glaza, A. Giełdoń, J. Ciarkowski, B. Lipińska,
Arch. Biochem. Biophys. 2017, 621, 6-23.

Photophysical and theoretical studies of diphenylacetylene derivatives with restricted rotation,
M. Szyszkowska, C. Czaplewski, W. Wiczk,
J. Mol. Structure 2017, 1138, 81-89.

Polymerization of chloro-p-xylylenes, quantum-chemical study,
C. Czaplewski, K. Smalara, A. Giełdoń, M. Bobrowski,
J.Mol.Model. 2017, 23, 40.

Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids,
A. Giełdoń, M. Bobrowski, A. Bielicka-Giełdoń, C. Czaplewski,
J.Mol.Liq. 2017, 225, 467–474.

Role of the sulfur to α-carbon thioether bridges in thurincin H,
M.A. Mozolewska, A.K. Sieradzan, A. Niadzvedstki, C. Czaplewski, A. Liwo, P. Krupa,
J. Biomol. Struct. Dyn. 2017, 35, 2868-2879.

Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field.
M. Mozolewska, P. Krupa, B. Zaborowski, A. Liwo, J. Lee, K. Joo, C. Czaplewski,
J. Chem. Inf. Model. 2016, 56, 2263-2279.

PEGylated substrates of NSP4 protease : a tool to study protease specificity
M. Wysocka, N. Gruba, R. Grzywa, A. Giełdoń, R. Bąchor, K. Brzozowski, M. Sieńczyk, J. Dieter, Z. Szewczuk, K. Rolka, A. Lesner.

Scientific Reports 2016, 6, art. no. 22856, 1-11

Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction
A.G. Lipska, S.R. Seidman, A.K. Sieradzan, A. Giełdoń, A. Liwo, H.A. Scheraga.

J. Chem. Phys. 2016, 144, art.no.184110, 1-11

Intra- and intersubunit changes accompanying thermal activation of the HtrA2(Omi) protease homotrimer
M. Jarząb, T. Wenta, D. Żurawa-Janicka, A. Polit, A. Giełdoń, M. Wysocka, P. Glaza, J. Skórko-Glonek, J. Ciarkowski, A. Lesner, B. Lipińska.

Biochimica et Biophysica Acta. Proteins and Proteomics 2016, 1864, 283-296

Distinct 3D architecture and dynamics of the human HtrA2(Omi) protease and its mutated variants
A. Giełdoń, D. Żurawa-Janicka, M. Jarząb, T. Wenta, P. Golik, G. Dubin, B. Lipińska, J. Ciarkowski.
Distinct 3D architecture and dynamics of the human HtrA2(Omi) protease and its mutated variants
PLoS One 2016, 11, e.0161526, 1-19

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.
P. Krupa, M.A. Mozolewska, M. Wiśniewska, Y. Yin, Y. He, A.K. Sieradzan, R. Ganzynkowicz, A.G. Lipska, A. Karczyńska, M. Ślusarz, R. Ślusarz, A. Giełdoń, C. Czaplewski, D. Jagieła, B. Zaborowski, H.A. Scheraga, A. Liwo, 
Bioinformatics 2016, 32, 3270–3278

Bladder cancer detection using a peptide substrate of the 20S proteasome.
N. Gruba, M. Wysocka, M. Brzezińska, D. Dębowski, M.Sieńczyk, E. Gorodkiewicz, T. Guszcz, C. Czaplewski, K. Rolka and A. Lesner, 
FEBS J. 2016, 283, 2929–2948

Temperature-dependent structure-property modeling of viscosity for ionic liquids.
M. Barycki, A. Sosnowska, A. Gajewicz, M. Bobrowski, D. Wileńska, P. Skurski, A. Giełdoń, C. Czaplewski, S. Uhl, E. Laux, T. Journot, L. Jeandupeux, H. Keppner, T. Puzyn.
Fluid Phase Equilibria 2016, 427, 9-17

Photophysical properties of symmetrically substituted diarylacetylenes and diarylbuta-1,3-diynes
I. Bylińska, M. Wierzbicka, C. Czaplewski, Wiesław Wiczk.
Photochem. Photobiol. Sci. 2016, 15, 45-56

A maximum-likelihood approach to force-field calibration.
B. Zaborowski, D. Jagieła, C. Czaplewski, A. Hałabis, A. Lewandowska, W. Żmudzińska, S. Ołdziej, A. Karczyńska, C. Omieczynski, T. Wirecki, A. Liwo.
J. Chem. Inf. Model. 2015, 55, 2050-2070

Common functionally important motions of the nucleotide-binding domain of Hsp70
E.I. Gołaś, C. Czaplewski, H.A. Scheraga, A. Liwo.
Proteins: Struct. Funct. Bioinf. 2015, 83, 282-299

Experimental and theoretical studies of spectroscopic properties of simple symmetrically substituted diphenylbuta-1,3-diyne derivatives.
Małgorzata Wierzbicka, Irena Bylińska, Artur Sikorski, Cezary Czaplewski, Wiesław Wiczk
Photochem Photobiol Sci. 2015, 14, 2251-2260

Experimental and theoretical studies of the spectroscopic properties of simple symmetrically substituted diphenylacetylene derivatives.
Małgorzata Wierzbicka, Irena Bylińska, Cezary Czaplewski, Wiesław Wiczk
RSC Adv. 2015, 5, 29294-29303

Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the United Residue (UNRES) force field for protein simulations
Adam K. Sieradzan, Paweł Krupa, Harold A. Scheraga, Adam Liwo, Cezary Czaplewski.
J. Chem. Theory. Comput. 2015, 11, 817-831

Prediction of protein structure by template-based modeling combined with the UNRES force field
Paweł Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Cezary Czaplewski, Adam Liwo.
J. Chem. Inf. Model. 2015, 55, 1271-1281

RASMOL AB - New functionalities in the program for structure analysis
Mateusz Pikora, Artur Giełdoń.
Acta Biochim. Pol. 2015, 62, 629-631

A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions
Adam Liwo, Maciej Baranowski, Cezary Czaplewski, Ewa Gołaś, Yi He, Dawid Jagieła, Paweł Krupa, Maciej Maciejczyk, Mariusz Makowski, Magdalena A. Mozolewska, Andrei Niadzvedtski, Stanisław Ołdziej, Harold A. Scheraga, Adam K. Sieradzan, Rafał Ślusarz, Tomasz Wirecki, Yanping Yin, Bartłomiej Zaborowski.
J. Mol. Model. 2014, 20, 1-15

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements
Rui Zhou, Gia G. Maisuradze, David Suñol, Toni Todorovski, Maria J. Macias, Yi Xiao, Harold A. Scheraga, Cezary Czaplewski, Adam Liwo.
Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 18243-18248

Rapid communication: Computational simulation and analysis of a candidate for the design of a novel silk-based biopolymer
Ewa I. Gołaś, Cezary Czaplewski.
Biopolymers. 2014, 101, 915-923

Solvatochromic studies of pull-push molecules containing dimethylaniline and aromatic hydrocarbon linked by an acetylene unit
Irena Bylińska, Małgorzata Wierzbicka, Cezary Czaplewski, Wiesław Wiczk.
RSC Adv. 2014, 4, 48783-48795

Towards mechanisms of nanotoxicity - interaction of gold nanoparticles with proteins and DNA
Paweł Krupa, Magdalena A. Mozolewska, Bakhtiyor Rasulev, Cezary Czaplewski, Jerzy Leszczynski.
TASK Quarterly. 2014, 18, 337-341

The LA loop as an important regulatory element of the HtrA (DegP) protease from Escherichia coli : structural and functional studies
Donata Figaj, Artur Giełdoń, Agnieszka Polit, Anna Sobiecka-Szkatuła, Tomasz Koper, Milena Denkiewicz, Bogdan Banecki, Adam Lesner, Jerzy Ciarkowski, Barbara Lipińska, Joanna Skórko-Glonek.
J. Biol. Chem. 2014, 289, 15880-15893

Preliminary studies on trigonelline as potential anti-Alzheimer disease agent : determination by hydrophilic interaction liquid chromatography and modeling of interactions with beta-amyloid.
Joanna Makowska, Damian Szczesny, Agnieszka Lichucka, Artur Giełdoń, Lech Chmurzyński, Roman Kaliszan.

J. Chromatogr. B. 2014, 968, 101-104

Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.
Krupa P, Sieradzan AK, Rackovsky S, Baranowski M, Ołdziej S, Scheraga HA, Liwo A, Czaplewski C.
J. Chem. Theory. Comput. 2013, 9, 4620-4632

Lessons from application of the UNRES force field to predictions of structures of CASP10 targets.
He Y, Mozolewska MA, Krupa P, Sieradzan AK, Wirecki TK, Liwo A, Kachlishvili K, Rackovsky S, Jagiela D, Ślusarz R, Czaplewski CR, Ołdziej S, Scheraga HA.
Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 14936-14941.

Acid-base properties of 3-[2-(pyridyl)benzoxazol-5-yl]alanine derivatives in the ground and excited state : experimental and theoretical studies
Agnieszka Lewandowska, Katarzyna Guzow, Dominik Wróblewski, Cezary Czaplewski, Wiesław Wiczk.
J. Photochem. Photobiol. A Chem. 2013, 258, 10-16

Photophysical properties of 3-[2-(N-phenylcarbazolyl)benzoxazol-5-yl]alanine derivatives--experimental and theoretical studies.
Guzow K, Czerwińska M, Ceszlak A, Kozarzewska M, Szabelski M, Czaplewski C, Łukaszewicz A, Kubicki AA, Wiczk W.
Photochem Photobiol Sci. 2013, 12, 284-297.

Temperature-induced changes of HtrA2(Omi) protease activity and structure.
Zurawa-Janicka D, Jarzab M, Polit A, Skorko-Glonek J, Lesner A, Gitlin A, Gieldon A, Ciarkowski J, Glaza P, Lubomska A, Lipinska B.
Cell Stress Chaperones. 2013, 18, 35-51.

Treść ostatnio zmodyfikowana przez: Artur Giełdoń
Treść wprowadzona przez: Artur Giełdoń
Ostatnia modyfikacja: 
poniedziałek, 16 lipca 2018 roku, 18:56