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ORCIDCezary Czaplewski
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2020 – today
- 2024
[j21]Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan
, Pawel Czarnul:
Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems. Comput. Phys. Commun. 298: 109112 (2024)- [j20]Mateusz Lesniewski, Maciej Pyrka, Cezary Czaplewski, Nguyen Truong Co, Yida Jiang, Zhou Gong, Chun Tang, Adam Liwo:
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures. J. Chem. Inf. Model. 64(4): 1377-1393 (2024) - 2023
- [j19]Adam K. Sieradzan, Jordi Sans-Duñó, Emilia A. Lubecka, Cezary Czaplewski, Agnieszka G. Lipska, Henryk Leszczynski, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo:
Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins. J. Comput. Chem. 44(4): 602-625 (2023) - [j18]Agnieszka G. Lipska, Adam K. Sieradzan, Cezary Czaplewski, Andrea D. Lipinska, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo:
Long-time scale simulations of virus-like particles from three human-norovirus strains. J. Comput. Chem. 44(16): 1470-1483 (2023) - 2021
- [j17]Pawel Krupa, Agnieszka S. Karczynska, Magdalena A. Mozolewska, Adam Liwo, Cezary Czaplewski:
UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations. Bioinform. 37(11): 1613-1615 (2021) - 2020
- [j16]Agnieszka S. Karczynska, Karolina Zieba, Urszula Uciechowska, Magdalena A. Mozolewska, Pawel Krupa, Emilia A. Lubecka, Agnieszka G. Lipska, Celina Sikorska, Sergey A. Samsonov, Adam K. Sieradzan, Artur Gieldon, Adam Liwo, Rafal Slusarz, Magdalena Slusarz, Jooyoung Lee, Keehyoung Joo, Cezary 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)
2010 – 2019
- 2018
- [j15]Cezary Czaplewski, Agnieszka S. Karczynska, Adam K. Sieradzan, Adam Liwo:
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics. Nucleic Acids Res. 46(Webserver-Issue): W304-W309 (2018) - [j14]Emilia A. Lubecka, Adam K. Sieradzan, Cezary Czaplewski, Pawel Krupa, Adam Liwo:
High Performance Computing with Coarse Grained Model of Biological Macromolecules. Supercomput. Front. Innov. 5(2): 63-75 (2018) - 2017
- [j13]Agnieszka S. Karczynska, Cezary Czaplewski, Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Adam Liwo:
Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins. J. Comput. Chem. 38(31): 2730-2746 (2017) - 2016
- [j12]Pawel Krupa, Magdalena A. Mozolewska, Marta Wisniewska, Yanping Yin, Yi He, Adam K. Sieradzan, Robert Ganzynkowicz, Agnieszka G. Lipska, Agnieszka S. Karczynska, Magdalena Slusarz, Rafal Slusarz, Artur Gieldon, Cezary Czaplewski, Dawid Jagiela, Bartlomiej Zaborowski, Harold A. Scheraga, Adam Liwo:
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinform. 32(21): 3270-3278 (2016) - [j11]Magdalena A. Mozolewska, Pawel Krupa, Bartlomiej Zaborowski, Adam Liwo, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski:
Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field. J. Chem. Inf. Model. 56(11): 2263-2279 (2016) - 2015
- [j10]Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Cezary Czaplewski, Adam Liwo:
Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field. J. Chem. Inf. Model. 55(6): 1271-1281 (2015) - [j9]Bartlomiej Zaborowski, Dawid Jagiela, Cezary Czaplewski, Anna Halabis, Agnieszka Lewandowska, Wioletta Zmudzinska, Stanislaw Oldziej, Agnieszka S. Karczynska, Christian Omieczynski, Tomasz K. Wirecki, Adam Liwo:
A Maximum-Likelihood Approach to Force-Field Calibration. J. Chem. Inf. Model. 55(9): 2050-2070 (2015) - 2010
- [c3]Stanislaw Oldziej, Cezary Czaplewski, Adam Liwo, Harold A. Scheraga:
Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations. BIBE 2010: 263-266
2000 – 2009
- 2006
- [j8]Maurizio Chinchio, Cezary Czaplewski, Stanislaw Oldziej, Harold A. Scheraga:
A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low-Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United-Residue Force Field. Multiscale Model. Simul. 5(4): 1175-1195 (2006) - [c2]Roman Wyrzykowski, Norbert Meyer, Tomasz Olas, Lukasz Kuczynski, Bogdan Ludwiczak, Cezary Czaplewski, Stanislaw Oldziej:
Meta-computations on the CLUSTERIX Grid. PARA 2006: 489-500 - 2005
- [j7]Kyoungrim Lee, Cezary Czaplewski, Seung-Yeon Kim, Jooyoung Lee:
An efficient molecular docking using conformational space annealing. J. Comput. Chem. 26(1): 78-87 (2005) - [j6]Marian Nanias, Maurizio Chinchio, Stanislaw Oldziej, Cezary Czaplewski, Harold A. Scheraga:
Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC. J. Comput. Chem. 26(14): 1472-1486 (2005) - 2002
- [j5]Harold A. Scheraga, Jaroslaw Pillardy, Adam Liwo, Jooyoung Lee, Cezary Czaplewski, Daniel R. Ripoll, William J. Wedemeyer, Yelena A. Arnautova:
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. J. Comput. Chem. 23(1): 28-34 (2002) - 2000
- [c1]Adam Liwo, Jaroslaw Pillardy, Cezary Czaplewski, Jooyoung Lee, Daniel R. Ripoll, Malgorzata Groth, Sylwia Rodziewicz-Motowidlo, Rajmund Kazmierkiewicz, Ryszard J. Wawak, Stanislaw Oldziej, Harold A. Scheraga:
UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms. RECOMB 2000: 193-200
1990 – 1999
- 1999
- [j4]Rajmund Kazmierkiewicz, Cezary Czaplewski, B. Lammek, Jerzy Ciarkowski:
Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories. J. Comput. Aided Mol. Des. 13(1): 21-33 (1999) - 1998
- [j3]Cezary Czaplewski, Rajmund Kazmierkiewicz, Jerzy Ciarkowski:
Molecular modeling of the human vasopressin V2 receptor/agonist complex. J. Comput. Aided Mol. Des. 12(3): 275-287 (1998) - [j2]Adam Liwo, Rajmund Kazmierkiewicz, Cezary Czaplewski, Malgorzata Groth, Stanislaw Oldziej, Ryszard J. Wawak, Shelly Rackovsky, Matthew R. Pincus, Harold A. Scheraga:
United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials. J. Comput. Chem. 19(3): 259-276 (1998) - 1997
- [j1]Rajmund Kazmierkiewicz, Cezary Czaplewski, B. Lammek, Jerzy Ciarkowski:
Molecular modeling of the neurophysin I/oxytocin complex. J. Comput. Aided Mol. Des. 11(1): 9-20 (1997)
Coauthor Index
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