Papers published in 2018
Papers published in 2019
A. Liwo, A.K. Sieradzan, C. Czaplewski, 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. In: Kister A. (eds) Protein Supersecondary Structures. Methods in Molecular Biology, vol 1958. Humana Press, New York, NY, pp. 133-146 (2019).
E.A. Lubecka, A.S. Karczyńska, A.G. Lipska, A.K. Sieradzan, K. Ziȩba, C. Sikorska, U. Uciechowska, S.A Samsonov, P. Krupa, M.A. Mozolewska, Ł. Golon, A. Giełdoń, C. Czaplewski, R. Ślusarz, M. Ślusarz, S.N. Crivelli, A. Liwo, Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment. J. Mol. Graph. Model. 92, 154-166 (2019).
J.E. Fajardo, R. Shrestha, N. Gil, A. Belsom, S.N. Crivelli, C. Czaplewski, K. Fidelis, S. Grudinin, M. Karasikov, A.S. Karczyńska, A. Kryshtafovych, A. Leitner, A. Liwo, E.A. Lubecka, B. Monastyrskyy, G. Pagès, J. Rappsilber, A.K. Sieradzan, C. Sikorska, E. Trabjerg, A. Fiser, Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. Proteins 87, 1283-1297 (2019).
M.F Lensink, G. Brysbaert, N. Nadzirin, S. Velankar, R.A.G. Chaleil, T. Gerguri, P.A. Bates, E. Laine, A. Carbone, S. Grudinin, R. Kong, R. Liu, X. Xu, H. Shi, S. Chang, M. Eisenstein, A. Karczynska, C. Czaplewski, E. Lubecka, A. Lipska, P. Krupa, M. Mozolewska, Ł. Golon, S. Samsonov, A. Liwo, et al. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. Proteins 87, 1200-1221 (2019).
Papers published in 2020
A Liwo, C Czaplewski, 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. J. Chem. Phys.152, 054902 (2020).
A.S. Karczyńska, K. Zięba, U. Uciechowska, M.A. Mozolewska, P. Krupa, E.A. Lubecka, A.G. Lipska, C. Sikorska, S.A. Samsonov, A.K. Sieradzan, A. Giełdoń, A. Liwo, R. Ślusarz, M. Ślusarz, J. Lee, K. Joo, C. Czaplewski, Improved consensus-fragment selection in template-assisted prediction of protein structures with the UNRES force field in CASP13. J. Chem. Inf. Model. 60(3), 1844-1864 (2020) doi:10.1021/acs.jcim.9b00864
K. Zięba, C. Czaplewski, A. Liwo, G. Graziano, Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models. Phys. Chem. Chem. Phys. 22(8), 4758-4771 (2020) doi:10.1039/C9CP06627F
A. Liwo, C. Czaplewski, A.K. Sieradzan, E.A. Lubecka, A.G. Lipska, Ł. Golon, A. Karczyńska, P. Krupa, M.A. Mozolewska, M. Makowski, R. Ganzynkowicz, A. Giełdoń, M. Maciejczyk, Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers. In: B. Strodel, B. Barz (eds.) Progress in Molecular Biology and Translational Science, vol 170, Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Academic Press, Cambridge, MA, pp. 73-122 (2020)
UNRES-Dock
UNRES-Dock extenstion for docking of two proteins with random starting orientations added to the UNRES server http://unres-server.chem.ug.edu.pl/
Papers published in 2021
M.F. Lensink, G. Brysbaert, T. Mauri, et al. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins 89( 12): 1800- 1823 (2021) doi:10.1002/prot.26222
A. Liwo, C. Czaplewski, A.K. Sieradzan, A.G. Lipska, S.A. Samsonov, R.K. Murarka, Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems. Biomolecules 11, 1347 (2021) doi:10.3390/biom11091347
A. Antoniak, I. Biskupek, K.K. Bojarski, C. Czaplewski, A. Giełdoń, M. Kogut, M.M. Kogut, P. Krupa, A.G. Lipska, A. Liwo, E.A. Lubecka, M. Marcisz, M. Maszota-Zieleniak, S.A. Samsonov, A.K. Sieradzan, M.J. Ślusarz, R. Ślusarz, P.A. Wesołowski, K. Ziȩba, Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment, J. Mol. Graph. Model. 108, 108008 (2021) doi:10.1016/j.jmgm.2021.108008
A. Kryshtafovych, J. Moult, W.M. Billings, et al. Modeling SARS-CoV-2 proteins in the CASP-commons experiment, Proteins 89 (12), 1987- 1996 (2021) doi:10.1002/prot.26231
C. Czaplewski, Z. Gong, E. Lubecka, K. Xue, C. Tang, A. Liwo, Recent developments in data-assisted modeling of flexible proteins, Front. Mol. Biosci. 8, 1-8 (2021) doi:10.3389/fmolb.2021.765562
M. Kogut, Z. Gong, C. Tang, A. Liwo, Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures, J. Comput. Chem. 42, 2054 (2021). https://doi.org/10.1002/jcc.26736
Papers published in 2022
A. Liwo, A.K. Sieradzan, A.S. Karczyńska, E.A. Lubecka, S.A. Samsonov, C. Czaplewski, P. Krupa, M. Mozolewska, Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry. In: Leszczynski J., Shukla M.K. (eds) Practical Aspects of Computational Chemistry V (2022), Springer, Cham. https://doi.org/10.1007/978-3-030-83244-5_2
A.K. Sieradzan, C. Czaplewski, P. Krupa, M.A. Mozolewska, A.S. Karczyńska, A.G. Lipska, E.A. Lubecka, E. Gołaś, T. Wirecki, M. Makowski, S. Ołdziej, A. Liwo, Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field. In: Muñoz V. (eds) Protein Folding. Methods in Molecular Biology, vol 2376 (2022), Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1716-8_23
I. Biskupek, A. Sieradzan, C. Czaplewski, A. Liwo, A. Lesner, A. Giełdoń, Theoretical investigation of the coronavirus SARS‐CoV‐2 (COVID-19) infection mechanism and selectivity, Molecules 27 (7), 2080 (2022). https://doi.org/10.3390/molecules27072080
R. Ślusarz, E. Lubecka, C. Czaplewski, A. Liwo, Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions, Fron. Mol.Biosci. 9, 1071428 (2022). https://doi: 10.3389/fmolb.2022.1071428
I. Biskupek, C. Czaplewski, J. Sawicka, E. Iłowska, M. Dzierżyńska, S. Rodziewicz-Motowidło, A. Liwo, Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model, Biomolecules 12(8), 1140 (2022). https://doi.org/10.3390/biom12081140
Papers published in 2023
A.K. Sieradzan, J. Sans‐Duñó, E.A. Lubecka, C. Czaplewski, A.G. Lipska, H. Leszczyński, K.M. Ocetkiewicz, J. Proficz, P. Czarnul, H. Krawczyk, A. Liwo, Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins, J. Comput. Chem. 44(4), 602 (2023). https://doi.org/10.1002/jcc.27026
A.G. Lipska, A.K. Sieradzan, C. Czaplewski, A.D. Lipińska, K.M. Ocetkiewicz, J. Proficz, P. Czarnul, H. Krawczyk, A. Liwo, Long‐time scale simulations of virus‐like particles from three human‐norovirus strains, J. Comput. Chem. 44(16), 1470 (2023) https://doi.org/10.1002/jcc.27087