Molecular modeling of the neurophysin I/oxytocin complex. - Rajmund Kazmierkiewicz; Cezary Czaplewski; B. Lammek; Jerzy Ciarkowski (J. Comput. Aided Mol. Des., 1997)

Molecular modeling of the human vasopressin V2 receptor/agonist complex. - Cezary Czaplewski; Rajmund Kazmierkiewicz; Jerzy Ciarkowski (J. Comput. Aided Mol. Des., 1998)

United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials. - Adam Liwo; Rajmund Kazmierkiewicz; Cezary Czaplewski; Malgorzata Groth; Stanislaw Oldziej; Ryszard J. Wawak; Shelly Rackovsky; Matthew R. Pincus; Harold A. Scheraga (J. Comput. Chem., 1998)

Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories. - Rajmund Kazmierkiewicz; Cezary Czaplewski; B. Lammek; Jerzy Ciarkowski (J. Comput. Aided Mol. Des., 1999)

UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms. - Adam Liwo; Jaroslaw Pillardy; Cezary Czaplewski; Jooyoung Lee 002; Daniel R. Ripoll; Malgorzata Groth; Sylwia Rodziewicz-Motowidlo; Rajmund Kazmierkiewicz; Ryszard J. Wawak; Stanislaw Oldziej; Harold A. Scheraga (RECOMB, 2000)

Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. - Harold A. Scheraga; Jaroslaw Pillardy; Adam Liwo; Jooyoung Lee 002; Cezary Czaplewski; Daniel R. Ripoll; William J. Wedemeyer; Yelena A. Arnautova (J. Comput. Chem., 2002)

An efficient molecular docking using conformational space annealing. - Kyoungrim Lee; Cezary Czaplewski; Seung-Yeon Kim; Jooyoung Lee 002 (J. Comput. Chem., 2005)

Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC. - Marian Nanias; Maurizio Chinchio; Stanislaw Oldziej; Cezary Czaplewski; Harold A. Scheraga (J. Comput. Chem., 2005)

Meta-computations on the CLUSTERIX Grid. - Roman Wyrzykowski; Norbert Meyer; Tomasz Olas; Lukasz Kuczynski; Bogdan Ludwiczak; Cezary Czaplewski; Stanislaw Oldziej (PARA, 2006)

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. - Maurizio Chinchio; Cezary Czaplewski; Stanislaw Oldziej; Harold A. Scheraga (Multiscale Model. Simul., 2006)

Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations. - Stanislaw Oldziej; Cezary Czaplewski; Adam Liwo; Harold A. Scheraga (BIBE, 2010)

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field. - Pawel Krupa; Magdalena A. Mozolewska; Keehyoung Joo; Jooyoung Lee 002; Cezary Czaplewski; Adam Liwo (J. Chem. Inf. Model., 2015)

A Maximum-Likelihood Approach to Force-Field Calibration. - Bartlomiej Zaborowski; Dawid Jagiela; Cezary Czaplewski; Anna Halabis; Agnieszka Lewandowska; Wioletta Zmudzinska; Stanislaw Oldziej; Agnieszka S. Karczynska; Christian Omieczynski; Tomasz K. Wirecki; Adam Liwo (J. Chem. Inf. Model., 2015)

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. - 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; et al. (Bioinform., 2016)

Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field. - Magdalena A. Mozolewska; Pawel Krupa; Bartlomiej Zaborowski; Adam Liwo; Jooyoung Lee 002; Keehyoung Joo; Cezary Czaplewski (J. Chem. Inf. Model., 2016)

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins. - Agnieszka S. Karczynska; Cezary Czaplewski; Pawel Krupa; Magdalena A. Mozolewska; Keehyoung Joo; Jooyoung Lee 002; Adam Liwo (J. Comput. Chem., 2017)

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics. - Cezary Czaplewski; Agnieszka S. Karczynska; Adam K. Sieradzan; Adam Liwo (Nucleic Acids Res., 2018)

High Performance Computing with Coarse Grained Model of Biological Macromolecules. - Emilia A. Lubecka; Adam K. Sieradzan; Cezary Czaplewski; Pawel Krupa; Adam Liwo (Supercomput. Front. Innov., 2018)

Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13. - 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; et al. (J. Chem. Inf. Model., 2020)

UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations. - Pawel Krupa; Agnieszka S. Karczynska; Magdalena A. Mozolewska; Adam Liwo; Cezary Czaplewski (Bioinform., 2021)

Long-time scale simulations of virus-like particles from three human-norovirus strains. - Agnieszka G. Lipska; Adam K. Sieradzan; Cezary Czaplewski; Andrea D. Lipinska; Krzysztof M. Ocetkiewicz; Jerzy Proficz; Pawel Czarnul; Henryk Krawczyk; Adam Liwo (J. Comput. Chem., 2023)

Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins. - 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 (J. Comput. Chem., 2023)

Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems. - Krzysztof M. Ocetkiewicz; Cezary Czaplewski; Henryk Krawczyk; Agnieszka G. Lipska; Adam Liwo; Jerzy Proficz; Adam K. Sieradzan; Pawel Czarnul (Comput. Phys. Commun., 2024)

Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures. - Mateusz Lesniewski; Maciej Pyrka; Cezary Czaplewski; Nguyen Truong Co; Yida Jiang; Zhou Gong; Chun Tang; Adam Liwo (J. Chem. Inf. Model., 2024)