C. Czaplewski

发表

Computational techniques for efficient conformational sampling of proteins.

A. Liwo, H. Scheraga, C. Czaplewski, 2008, Current opinion in structural biology.

United‐residue force field for off‐lattice protein‐structure simulations: III. Origin of backbone hydrogen‐bonding cooperativity in united‐residue potentials

A. Liwo, M. Pincus, H. Scheraga, 1998 .

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.

A. Liwo, H. Scheraga, C. Czaplewski, 2009, Journal of chemical theory and computation.

Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field

A. Liwo, H. Scheraga, C. Czaplewski, 2001 .

Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field

A. Liwo, H. Scheraga, C. Czaplewski, 2008 .

Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

Adam K. Sieradzan, Tomasz K. Wirecki, S. Rackovsky, 2013, Proceedings of the National Academy of Sciences.

Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.

A. Liwo, H. Scheraga, C. Czaplewski, 2007, The journal of physical chemistry. B.

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

A. Liwo, H. Scheraga, K. Gibson, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Conformation-Family Monte Carlo (CFMC): An Efficient Computational Method for Identifying the Low-Energy States of a Macromolecule.

H. Scheraga, W. Wedemeyer, C. Czaplewski, 2000 .

Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.

Adam Liwo, Cezary Czaplewski, Harold A Scheraga, 2010, The journal of physical chemistry. A.

1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins

A. Liwo, H. Scheraga, C. Czaplewski, 2012 .

Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain.

Dana S Kleinerman, A. Liwo, H. Scheraga, 2008, The Journal of chemical physics.

A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions

Adam K. Sieradzan, Tomasz K. Wirecki, A. Liwo, 2014, Journal of Molecular Modeling.

Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers.

Adam K. Sieradzan, Agnieszka S. Karczynska, A. Liwo, 2020, Progress in molecular biology and translational science.

Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing

H. Scheraga, Jooyoung Lee, C. Czaplewski, 2001 .

A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field

A. Liwo, H. Scheraga, C. Czaplewski, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems†

A. Liwo, H. Scheraga, C. Czaplewski, 2004 .

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization

A. Liwo, H. Scheraga, C. Czaplewski, 2004 .

Coarse-Grained Models of Proteins: Theory and Applications

A. Liwo, H. Scheraga, C. Czaplewski, 2011 .

Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics.

A. Liwo, H. Scheraga, C. Czaplewski, 2012, Journal of chemical theory and computation.

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

A. Liwo, H. Scheraga, C. Czaplewski, 2014, Proceedings of the National Academy of Sciences.

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, A. Liwo, H. Scheraga, 2015, Journal of chemical theory and computation.

Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets.

Agnieszka S. Karczynska, A. Liwo, Jooyoung Lee, 2018, Journal of molecular graphics & modelling.

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

A. Liwo, C. Czaplewski, S. Dunin-Horkawicz, 2018, PloS one.

Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment.

Adam K. Sieradzan, Agnieszka S. Karczynska, A. Liwo, 2019, Journal of molecular graphics & modelling.

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation.

Adam K. Sieradzan, A. Liwo, C. Czaplewski, 2019, The Journal of chemical physics.

The protein folding problem: global optimization of the force fields.

A. Liwo, H. Scheraga, C. Czaplewski, 2004, Frontiers in bioscience : a journal and virtual library.

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins

Adam Liwo, Jaroslaw Pillardy, Harold A. Scheraga, 2004 .

Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation

Adam Liwo, Jaroslaw Pillardy, Harold A. Scheraga, 2004 .

Can cooperativity in hydrophobic association be reproduced correctly by implicit solvation models

A. Liwo, H. Scheraga, C. Czaplewski, 2002 .

Chemoinformatics Methods for Studying Biomolecules

A. Liwo, Jooyoung Lee, C. Czaplewski, 2016 .

The Protein Folding Problem

A. Liwo, H. Scheraga, R. Elber, 2006 .

Molecular dynamics simulation studies of lipid bilayer systems.

C. Czaplewski, T. Róg, K. Murzyn, 2000, Acta biochimica Polonica.

Potential of mean force of association of large hydrophobic particles: toward the nanoscale limit.

A. Liwo, H. Scheraga, C. Czaplewski, 2010, The journal of physical chemistry. B.

Molecular dynamics simulations of the growth of poly(chloro-para-xylylene) films

C. Czaplewski, M. Bobrowski, A. Giełdoń, 2011, Journal of molecular modeling.

Role of the sulfur to α-carbon thioether bridges in thurincin H

Adam K. Sieradzan, A. Liwo, C. Czaplewski, 2017, Journal of biomolecular structure & dynamics.

Experimental and theoretical studies of the spectroscopic properties of simple symmetrically substituted diphenylacetylene derivatives

C. Czaplewski, W. Wiczk, M. Wierzbicka, 2015 .

Photophysical properties of symmetrically substituted diarylacetylenes and diarylbuta-1,3-diynes

C. Czaplewski, W. Wiczk, M. Wierzbicka, 2016, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

Evolution of physics‐based methodology for exploring the conformational energy landscape of proteins

Adam Liwo, Jooyoung Lee, Jaroslaw Pillardy, 2002, J. Comput. Chem..

Reply to “Comment on ‘Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions'” by B. P. van Eijck and J. Kroon

H. Scheraga, W. Wedemeyer, C. Czaplewski, 2000 .

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.

A. Liwo, C. Czaplewski, 2020, The Journal of chemical physics.

Common functionally important motions of the nucleotide‐binding domain of Hsp70

A. Liwo, H. Scheraga, C. Czaplewski, 2015, Proteins.

A DFT/TD DFT study of the structure and spectroscopic properties of 5-methyl-2-(8-quinolinyl)benzoxazole and its complexes with Zn(II) ion.

C. Czaplewski, W. Wiczk, Katarzyna Guzow, 2010, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models.

A. Liwo, C. Czaplewski, G. Graziano, 2020, Physical chemistry chemical physics : PCCP.

Bladder cancer detection using a peptide substrate of the 20S proteasome

C. Czaplewski, M. Sieńczyk, A. Lesner, 2016, The FEBS journal.

Conformational studies of vasopressin and mesotocin using NMR spectroscopy and molecular modelling methods. Part II: studies in the SDS micelle

C. Czaplewski, E. Sikorska, M. Oleszczuk, 2008, Journal of peptide science : an official publication of the European Peptide Society.

Fluorescence decay time distribution analysis of cyclic enkephalin analogues. Influence of the solvents and configuration of amino acids in position 2 and 3 on changes in conformation.

A. Liwo, C. Czaplewski, M. Groth, 1999, Acta biochimica Polonica.

The Two Aspects of the Protein Folding Problem

A. Liwo, H. Scheraga, C. Czaplewski, 2006 .

Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis

C. Czaplewski, A. Giełdoń, A. Lesner, 2019, International journal of molecular sciences.

Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model

A. Liwo, C. Czaplewski, S. Rodziewicz-Motowidło, 2022, Biomolecules.

Temperature-dependent structure-property modeling of viscosity for ionic liquids

A. Sosnowska, T. Puzyn, Maciej Barycki, 2016 .

EPCC-SS 96-02 Simulation of the crystal structure of ice

C. Czaplewski, 2007 .

Experimental and theoretical studies of spectroscopic properties of simple symmetrically substituted diphenylbuta-1,3-diyne derivatives

C. Czaplewski, W. Wiczk, M. Wierzbicka, 2015, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

Solvatochromic studies of pull–push molecules containing dimethylaniline and aromatic hydrocarbon linked by an acetylene unit

C. Czaplewski, W. Wiczk, M. Wierzbicka, 2014 .

Use of NMR and fluorescence spectroscopy as well as theoretical conformational analysis in conformation-activity studies of cyclic enkephalin analogues.

A. Liwo, L. Lankiewicz, C. Czaplewski, 2004, Current topics in medicinal chemistry.

Photophysical and theoretical studies of diphenylacetylene derivatives with restricted rotation

C. Czaplewski, W. Wiczk, Małgorzata A. Szyszkowska, 2017 .

Conformation-activity relationships of cyclo-constrained mu/delta opioid agonists derived from the N-terminal tetrapeptide segment of dermorphin/deltorphin.

C. Czaplewski, P. Schiller, S. Rodziewicz-Motowidło, 2009, Advances in experimental medicine and biology.

Deltorphin analogs restricted via a urea bridge: structure and opioid activity.

C. Czaplewski, P. Schiller, S. Rodziewicz-Motowidło, 2009, Advances in experimental medicine and biology.

Conformation‐activity relationships of cyclo‐constrained µ/δ opioid agonists derived from the N‐terminal tetrapeptide segment of dermorphin/deltorphin

C. Czaplewski, J. Ciarkowski, Sylwia Rodziewicz‐MotowidŁo, 2008, Journal of peptide science : an official publication of the European Peptide Society.

Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins

Adam K. Sieradzan, A. Liwo, C. Czaplewski, 2022, J. Comput. Chem..

Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles.

A. Liwo, H. Scheraga, C. Czaplewski, 2003, Biophysical chemistry.

Comment on “Anti-cooperativity in hydrophobic interactions: A simulation study of spatial dependence of three-body effects and beyond” [J. Chem. Phys. 115, 1414 (2001)]

A. Liwo, H. Scheraga, C. Czaplewski, 2002 .

Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions

A. Liwo, C. Czaplewski, R. Ślusarz, 2022, Frontiers in Molecular Biosciences.

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α + β Proteins

A. Liwo, H. Scheraga, C. Czaplewski, 2009 .

Solution conformational study of Scyliorhinin I analogues with conformational constraints by two-dimensional NMR and theoretical conformational analysis.

A. Liwo, C. Czaplewski, J. Zabrocki, 2000, The journal of peptide research : official journal of the American Peptide Society.

Determination of conformational equilibrium of peptides in solution by NMR spectroscopy and theoretical conformational analysis: application to the calibration of mean-field solvation models.

A. Liwo, C. Czaplewski, M. Groth, 2001, Biopolymers.

Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids

C. Czaplewski, M. Bobrowski, A. Giełdoń, 2017 .

Acid–base properties of 3-[2-(pyridyl)benzoxazol-5-yl]alanine derivatives in the ground and excited state. Experimental and theoretical studies

C. Czaplewski, A. Lewandowska, W. Wiczk, 2013 .

The photophysics of β-homo-tyrosine and its simple derivatives

A. Liwo, C. Czaplewski, S. Ołdziej, 1996 .

Photophysical properties of 3-[2-(N-phenylcarbazolyl)benzoxazol-5-yl]alanine derivatives--experimental and theoretical studies.

C. Czaplewski, W. Wiczk, Katarzyna Guzow, 2013, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field

Adam Liwo, Keehyoung Joo, Jooyoung Lee, 2016, J. Chem. Inf. Model..

Comparison of two approaches to potential of mean force calculations of hydrophobic association: particle insertion and weighted histogram analysis methods

A. Liwo, C. Czaplewski, Sebastian Kalinowski, 2005 .

Reaction of 4-benzylidene-2-methyl-5-oxazolone with amines, Part 2: Influence of substituents in para-position in the phenyl ring and a substituent on amine nitrogen atom on the reaction kinetics

C. Czaplewski, B. Banecki, W. Wiczk, 2002 .

Protein structure prediction with the UNRES force‐field using Replica‐Exchange Monte Carlo‐with‐Minimization; Comparison with MCM, CSA, and CFMC

Cezary Czaplewski, Marian Nanias, Maurizio Chinchio, 2005, J. Comput. Chem..

Polymerization of chloro-p-xylylenes, quantum-chemical study

C. Czaplewski, M. Bobrowski, A. Giełdoń, 2017, Journal of Molecular Modeling.

Molecular simulation study of cooperativity in hydrophobic association

H A Scheraga, A. Liwo, H. Scheraga, 2000, Protein science : a publication of the Protein Society.

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Jeffrey J. Gray, Panagiotis I. Koukos, Johnathan D. Guest, 2021, Proteins.

Long‐time scale simulations of virus‐like particles from three human‐norovirus strains

Adam K. Sieradzan, A. Liwo, C. Czaplewski, 2023, Journal of computational chemistry.

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Elodie Laine, Alessandra Carbone, Adam Liwo, 2019, Proteins.

Membrane Initiated Gelsolin Amyloid Formation

A. Liwo, P. Janmey, C. Czaplewski, 2006 .

Towards gelsolin amyloid formation

A. Liwo, P. Janmey, C. Czaplewski, 2004, Biopolymers.

Deltorphin analogs restricted via a urea bridge: structure and opioid activity

C. Czaplewski, P. Schiller, S. Rodziewicz-Motowidło, 2008, Journal of peptide science : an official publication of the European Peptide Society.

G Protein-coupled receptor–bioligand interactions modeled in a phospholipid bilayer

C. Czaplewski, M. Pasenkiewicz-Gierula, J. Ciarkowski, 1999 .

Molecular modeling of the human vasopressin V2 receptor/agonist complex

Cezary Czaplewski, Rajmund Kazmierkiewicz, Jerzy Ciarkowski, 1998, J. Comput. Aided Mol. Des..

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

Adam K. Sieradzan, A. Liwo, C. Czaplewski, 2021, Biomolecules.

Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds.

Adam Liwo, Cezary Czaplewski, Stanislaw Oldziej, 2004, Protein engineering, design & selection : PEDS.

Recent Developments in Data-Assisted Modeling of Flexible Proteins

A. Liwo, C. Czaplewski, E. Lubecka, 2021, Frontiers in Molecular Biosciences.

Design of a knowledge-based force field for off-lattice simulations of protein structure.

A. Liwo, C. Czaplewski, R. Kazmierkiewicz, 1997, Acta biochimica Polonica.

Multiple β‐sheet molecular dynamics of amyloid formation from two ABl‐SH3 domain peptides

A. Liwo, C. Czaplewski, S. Ventura, 2012, Biopolymers.

Rapid communication: Computational simulation and analysis of a candidate for the design of a novel silk‐based biopolymer

C. Czaplewski, Ewa I. Golas, 2014, Biopolymers.

Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods

Adam Liwo, Cezary Czaplewski, Rajmund Kaźmierkiewicz, 1999 .

Recent improvements in prediction of protein structure by global optimization of a potential energy function

Adam Liwo, Harold A. Scheraga, Cezary Czaplewski, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field

Adam Liwo, Keehyoung Joo, Cezary Czaplewski, 2015, J. Chem. Inf. Model..

Implication of the disulfide bridge in trypsin inhibitor SFTI-1 in its interaction with serine proteinases.

C. Czaplewski, A. Lesner, K. Rolka, 2010, Bioorganic & medicinal chemistry.

Theoretical investigation of the structural insights of the interactions of γ-Fe2O3 nanoparticle with (EMIM TFSI) ionic liquid

Adam K. Sieradzan, C. Czaplewski, M. Bobrowski, 2021 .

Theoretical Investigation of the Coronavirus SARS-CoV-2 (COVID-19) Infection Mechanism and Selectivity

Adam K. Sieradzan, A. Liwo, C. Czaplewski, 2022, Molecules.

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Adam Liwo, Yi He, Jilong Li, 2018, Scientific Reports.

Molecular dynamics study of amyloid formation of two Abl‐SH3 domain peptides

A. Liwo, C. Czaplewski, S. Ventura, 2006, Journal of peptide science : an official publication of the European Peptide Society.

Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories

Cezary Czaplewski, Rajmund Kazmierkiewicz, Jerzy Ciarkowski, 1999, J. Comput. Aided Mol. Des..

Molecular dynamics study of a gelsolin‐derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5‐bisphosphate

A. Liwo, P. Janmey, C. Czaplewski, 2003, Biopolymers.

Prediction of protein structure with the coarse‐grained UNRES force field assisted by small X‐ray scattering data and knowledge‐based information

Adam Liwo, Cezary Czaplewski, Agnieszka S Karczyńska, 2018, Proteins.

Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.

Adam K. Sieradzan, Agnieszka S. Karczynska, Tomasz K. Wirecki, 2021, Methods in molecular biology.

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics

Adam Liwo, Cezary Czaplewski, Adam K. Sieradzan, 2018, Nucleic Acids Res..

A Maximum-Likelihood Approach to Force-Field Calibration

Adam Liwo, Cezary Czaplewski, Agnieszka Lewandowska, 2015, J. Chem. Inf. Model..

Conformation-family Monte Carlo: A new method for crystal structure prediction

Jaroslaw Pillardy, Harold A. Scheraga, Cezary Czaplewski, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Influence of solvents and leucine configuration at position 5 on tryptophan fluorescence in cyclic enkephalin analogues.

C. Czaplewski, M. Groth, W. Wiczk, 2001, Biopolymers.

Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain

A. Liwo, P. Janmey, C. Czaplewski, 2003 .

Molecular origin of anticooperativity in hydrophobic association.

A. Liwo, H. Scheraga, C. Czaplewski, 2005, The journal of physical chemistry. B.

Influence of solvent and configuration of residues at positions 2 and 3 on distance and mobility of pharmacophore groups at positions 1 and 4 in cyclic enkephalin analogues.

C. Czaplewski, M. Groth, J. Karolczak, 2001, Biopolymers.

Binding modes of a new epoxysuccinyl-peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity?

M. Jaskólski, C. Czaplewski, M. Kozak, 1999, Biochimica et biophysica acta.

Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field.

Cezary Czaplewski, Marian Nanias, Harold A Scheraga, 2006, Journal of chemical theory and computation.

Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment.

Adam K. Sieradzan, A. Liwo, C. Czaplewski, 2021, Journal of molecular graphics & modelling.

Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13

Adam Liwo, Keehyoung Joo, Cezary Czaplewski, 2020, J. Chem. Inf. Model..

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11

Adam Liwo, Yi He, Harold A. Scheraga, 2016, Bioinform..

Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.

Adam Liwo, Cezary Czaplewski, Philip D. Blood, 2010, Journal of chemical theory and computation.

Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach

A. Liwo, C. Czaplewski, Xu-biao Peng, 2023, Biomolecules.

UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales

Adam K. Sieradzan, A. Liwo, C. Czaplewski, 2023, Bioinformatics.

High Performance Computing with Coarse Grained Model of Biological Macromolecules

Adam Liwo, Cezary Czaplewski, Adam K. Sieradzan, 2018, Supercomput. Front. Innov..

Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer.

Adam K. Sieradzan, A. Liwo, C. Czaplewski, 2019, The journal of physical chemistry. B.

Meta-computations on the CLUSTERIX Grid

Norbert Meyer, Roman Wyrzykowski, Tomasz Olas, 2006, PARA.

Molecular modeling of the neurophysin I/oxytocin complex

Cezary Czaplewski, Rajmund Kazmierkiewicz, Jerzy Ciarkowski, 1997, J. Comput. Aided Mol. Des..

Molecular dynamics of a vasopressin V2 receptor in a phospholipid bilayer membrane.

C. Czaplewski, M. Pasenkiewicz-Gierula, J. Ciarkowski, 1999, Journal of receptor and signal transduction research.

Conformational studies of cyclic enkephalin analogues with L- or D-proline in position 3.

A. Liwo, C. Czaplewski, M. Groth, 2002, Biopolymers.

Maximum entropy approach to the determination of solution conformation of flexible polypeptides by global conformational analysis and NMR spectroscopy – Application to DNS1-c-[d-A2bu2, Trp4,Leu5]- enkephalin and DNS1-c-[d-A2bu2, Trp4, d-Leu5]enkephalin

A. Liwo, A. Liwo, C. Czaplewski, 1999, Journal of biomolecular NMR.

Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.

Adam Liwo, Harold A. Scheraga, Cezary Czaplewski, 2013, Journal of chemical theory and computation.

UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations

Adam Liwo, Cezary Czaplewski, Magdalena A. Mozolewska, 2020, Bioinform..

Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13

Adam Liwo, Juri Rappsilber, J Eduardo Fajardo, 2019, Proteins.

Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field.

A. Liwo, H. Scheraga, C. Czaplewski, 2007, Journal of chemical theory and computation.

Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field.

Adam Liwo, Hujun Shen, Cezary Czaplewski, 2008, Journal of chemical theory and computation.

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

Cezary Czaplewski, Maurizio Chinchio, Stanislaw Oldziej, 2006, Multiscale Model. Simul..

UNRES: a united-residue force field for energy-based prediction of protein structure—orgin and significance of multibody terms

Adam Liwo, Jooyoung Lee, Jaroslaw Pillardy, 2000, RECOMB '00.

Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry

Adam K. Sieradzan, Agnieszka S. Karczynska, A. Liwo, 2021, Practical Aspects of Computational Chemistry V.

Molecular modeling of the oxytocin receptor/bioligand interactions.

C. Czaplewski, J. Ciarkowski, E. Politowska, 1999, Acta biochimica Polonica.

Theoretical study of polymerization mechanism of p-xylylene based polymers.

C. Czaplewski, M. Bobrowski, J. Rybicki, 2010, The journal of physical chemistry. A.

Conformation-Family Monte Carlo (CFMC): An Efficient Computational Method for Identifying the Low-Energy States of a Macromolecule

Jaroslaw Pillardy, Harold A. Scheraga, Cezary Czaplewski, 2000 .

Global optimization-based method for deriving intermolecular potential parameters for crystals

Jaroslaw Pillardy, Harold A. Scheraga, Cezary Czaplewski, 2003 .

Molecular modelling of the vasopressin V2 receptor/antagonist interactions.

C. Czaplewski, R. Kazmierkiewicz, J. Ciarkowski, 1998, Acta biochimica Polonica.

Computational techniques for efficient conformational sampling of proteins.

A. Liwo, H. Scheraga, C. Czaplewski, 2008, Current opinion in structural biology.

Ergodicity and model quality in template‐restrained canonical and temperature/Hamiltonian replica exchange coarse‐grained molecular dynamics simulations of proteins

Adam Liwo, Keehyoung Joo, Jooyoung Lee, 2017, J. Comput. Chem..

Pragmatic Coarse-Graining of Proteins: Models and Applications.

Adam K. Sieradzan, Paulo C. T. Souza, S. Pantano, 2023, Journal of chemical theory and computation.

Molecular dynamics simulation studies of lipid bilayer systems.

C. Czaplewski, T. Róg, K. Murzyn, 2000, Acta biochimica Polonica.

Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

Johnathan D. Guest, Adam K. Sieradzan, Charles W Christoffer, 2023, Proteins.

Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches

Adam K. Sieradzan, C. Czaplewski, A. Lipska, 2023, The journal of physical chemistry letters.

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.

Adam K. Sieradzan, A. Liwo, C. Czaplewski, 2019, Methods in molecular biology.

Mesoscopic Dynamics with the UNRES Force Field - a Tool for Studying the Kinetics and Thermodynamics of Protein Folding

A. Liwo, H. Scheraga, C. Czaplewski, 2007 .

THE PROTEIN FOLDING PROBLEM: GLOBAL OPTIMIZATION OF FORCE FIELDS

A. Liwo, H. Scheraga, C. Czaplewski, 2005 .

United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials

Adam Liwo, Harold A. Scheraga, Cezary Czaplewski, 1998, J. Comput. Chem..

Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13

Adam K. Sieradzan, Agnieszka S. Karczynska, A. Liwo, 2020, Proteins.

Multiplexed-Replica Exchange Molecular Dynamics with the UNRES Force-Field as an Effective Method for Exploring the Conformational Energy Landscape of Proteins.

G. Ulrich Nienhaus, Hans Frauenfelder, A. Liwo, 2006 .

Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures.

Adam Liwo, Mariusz Makowski, Cezary Czaplewski, 2009, Protein engineering, design & selection : PEDS.

Evolution of Experimental and Theoretical Determinations of Protein Structure and Protein Folding Pathways

A. Liwo, H. Scheraga, C. Czaplewski, 2007 .

Vasopressin V2 receptor/bioligand interactions

C. Czaplewski, R. Kazmierkiewicz, J. Ciarkowski, 1998, Letters in Peptide Science.

Implication of the disulfide bridge in trypsin inhibitor SFTI-1 in its interaction with serine proteinases.

C. Czaplewski, A. Lesner, K. Rolka, 2010, Bioorganic & medicinal chemistry.

Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems

C. Czaplewski, A. Lipska, P. Czarnul, 2024, Computer Physics Communications.

The ECEPP package for conformational analysis of polypeptides

A. Liwo, C. Czaplewski, D. Ripoll, 1999 .