Cezary Czaplewski

25 papers B 1C 1Journal 22Unranked 1
YearRankTypeTitle / Venue / Authors
2024 J jnl
Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.
J. Chem. Inf. Model.
Mateusz Lesniewski, Maciej Pyrka, Cezary Czaplewski, Nguyen Truong Co, Yida Jiang, Zhou Gong, Chun Tang, Adam Liwo
2024 J jnl
Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems.
Comput. Phys. Commun.
Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Pawel Czarnul
2023 J jnl
Long-time scale simulations of virus-like particles from three human-norovirus strains.
J. Comput. Chem.
Agnieszka G. Lipska, Adam K. Sieradzan, Cezary Czaplewski, Andrea D. Lipinska, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Pawel Czarnul, Henryk Krawczyk, Adam Liwo
2023 J jnl
Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins.
J. Comput. Chem.
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
2023 J jnl
UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales.
Bioinform.
Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Pawel Czarnul
2021 J jnl
UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations.
Bioinform.
Pawel Krupa, Agnieszka S. Karczynska, Magdalena A. Mozolewska, Adam Liwo, Cezary Czaplewski
2020 J jnl
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.
J. Chem. Inf. Model.
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
2018 J jnl
High Performance Computing with Coarse Grained Model of Biological Macromolecules.
Supercomput. Front. Innov.
Emilia A. Lubecka, Adam K. Sieradzan, Cezary Czaplewski, Pawel Krupa, Adam Liwo
2018 J jnl
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.
Nucleic Acids Res.
Cezary Czaplewski, Agnieszka S. Karczynska, Adam K. Sieradzan, Adam Liwo
2017 J jnl
Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.
J. Comput. Chem.
Agnieszka S. Karczynska, Cezary Czaplewski, Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Adam Liwo
2016 J jnl
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.
Bioinform.
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
2016 J jnl
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.
Magdalena A. Mozolewska, Pawel Krupa, Bartlomiej Zaborowski, Adam Liwo, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski
2015 J jnl
A Maximum-Likelihood Approach to Force-Field Calibration.
J. Chem. Inf. Model.
Bartlomiej Zaborowski, Dawid Jagiela, Cezary Czaplewski, Anna Halabis, Agnieszka Lewandowska, Wioletta Zmudzinska, Stanislaw Oldziej, Agnieszka S. Karczynska, Christian Omieczynski, Tomasz K. Wirecki, Adam Liwo
2015 J jnl
Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field.
J. Chem. Inf. Model.
Pawel Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Cezary Czaplewski, Adam Liwo
2010 C conf
Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations.
BIBE
Stanislaw Oldziej, Cezary Czaplewski, Adam Liwo, Harold A. Scheraga
2006 J jnl
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.
Maurizio Chinchio, Cezary Czaplewski, Stanislaw Oldziej, Harold A. Scheraga
2006 — conf
Meta-computations on the CLUSTERIX Grid.
PARA
Roman Wyrzykowski, Norbert Meyer, Tomasz Olas, Lukasz Kuczynski, Bogdan Ludwiczak, Cezary Czaplewski, Stanislaw Oldziej
2005 J jnl
An efficient molecular docking using conformational space annealing.
J. Comput. Chem.
Kyoungrim Lee, Cezary Czaplewski, Seung-Yeon Kim, Jooyoung Lee
2005 J jnl
Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.
J. Comput. Chem.
Marian Nanias, Maurizio Chinchio, Stanislaw Oldziej, Cezary Czaplewski, Harold A. Scheraga
2002 J jnl
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins.
J. Comput. Chem.
Harold A. Scheraga, Jaroslaw Pillardy, Adam Liwo, Jooyoung Lee, Cezary Czaplewski, Daniel R. Ripoll, William J. Wedemeyer, Yelena A. Arnautova
2000 B conf
UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms.
RECOMB
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
1999 J jnl
Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories.
J. Comput. Aided Mol. Des.
Rajmund Kazmierkiewicz, Cezary Czaplewski, B. Lammek, Jerzy Ciarkowski
1998 J jnl
Molecular modeling of the human vasopressin V2 receptor/agonist complex.
J. Comput. Aided Mol. Des.
Cezary Czaplewski, Rajmund Kazmierkiewicz, Jerzy Ciarkowski
1998 J jnl
United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials.
J. Comput. Chem.
Adam Liwo, Rajmund Kazmierkiewicz, Cezary Czaplewski, Malgorzata Groth, Stanislaw Oldziej, Ryszard J. Wawak, Shelly Rackovsky, Matthew R. Pincus, Harold A. Scheraga
1997 J jnl
Molecular modeling of the neurophysin I/oxytocin complex.
J. Comput. Aided Mol. Des.
Rajmund Kazmierkiewicz, Cezary Czaplewski, B. Lammek, Jerzy Ciarkowski