List of works - Cezary Czaplewski

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.

scientific article published on 3 December 2009

A Maximum-Likelihood Approach to Force-Field Calibration.

scientific article published on 11 August 2015

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 f

scientific article published on 01 April 2019

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

scientific article

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

scientific article

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

scientific article

An efficient molecular docking using conformational space annealing

scientific article published on 01 January 2005

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

scientific article published on March 2009

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

scientific article published on 07 October 2019

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

scientific article published on 03 January 2020

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

scientific article published on 01 May 1999

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

scientific article published on 21 June 2016

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

scientific article published on 25 October 2019

Charge loss in gas-phase multiply negatively charged oligonucleotides

scientific article published on January 2005

Coarse-Grained Models of Proteins: Theory and Applications

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

scientific article

Computational techniques for efficient conformational sampling of proteins

scientific article published on 22 January 2008

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

scientific article

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

scientific article published in January 2009

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

scientific article published in April 2002

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

scientific article published in January 2008

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

scientific article published on July 2008

Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes

article

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

scientific article

Dynamics study on single and multiple β-sheets

article

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

scientific article

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

scientific article published on 26 July 2019

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

scientific article published on 01 January 2002

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

scientific article published on 01 December 2015

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

scientific article published on 10 September 2019

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

scientific article published on 01 February 2020

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

scientific article

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

scientific article published on 01 January 2019

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

scientific article published on 01 February 2020

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.

scientific article published on 20 April 2018

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

scientific article published on August 2008

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.

scientific article

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

scientific article published on June 2008

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

scientific article published on 29 October 2010

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

scientific article published on 11 February 2020

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

article published in 2004

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

scientific article

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.

scientific article published in September 2001

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

scientific article

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

scientific article

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.

scientific article

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

scientific article published on 01 January 1999

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

scientific article

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

scientific article published in January 2003

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

scientific article

Molecular modeling of the human vasopressin V2 receptor/agonist complex

scientific article published on 01 May 1998

Molecular origin of anticooperativity in hydrophobic association

scientific article published on 01 April 2005

Molecular simulation study of cooperativity in hydrophobic association

scientific article published in June 2000

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

scientific article published on 01 September 2003

Molecular simulations of rhodopsin tetrameter.

scientific article

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

scientific article published in January 2012

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models

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

article

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

article by Stanislaw Oldziej et al published October 2004 in Journal of Physical Chemistry

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

article

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

scientific article

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

scientific article published on 19 September 2012

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

scientific article published on 30 November 2015

Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations

scientific article

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

scientific article (publication date: February 2017)

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

scientific article

Potential of mean force of hydrophobic association: dependence on solute size.

scientific article published on 22 August 2007

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

scientific article

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

scientific article published on 14 November 2017

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

scientific article

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

scientific article published on 25 September 2019

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

scientific article

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

scientific article published on 01 September 2014

Recent Developments in Data-Assisted Modeling of Flexible Proteins

publication published on 24 December 2021

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

scientific article

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

scientific article published on January 2006

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

scientific article published on 11 September 2016

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

scientific article published on 24 February 2020

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. 3. Calculation and Parameterization of the Potentials of Mean Force of Pairs of Identical Hydrophobic Side Chains

article

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains

scientific article published on 14 August 2008

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

scientific article

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

scientific article

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

The investigation of the effects of counterions in protein dynamics simulations

scientific article published on 01 October 2001

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

scientific article published in December 1996

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

scientific article

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

scientific article published in April 2010

Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations

Towards gelsolin amyloid formation

scientific article published on 01 January 2004

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.

scientific article

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

scientific article published in July 2018

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

scientific article published on 18 October 2020

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

scientific article published on January 2004

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

scientific article

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

scientific article published on 24 May 2018

List of works by Cezary Czaplewski

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.

A Maximum-Likelihood Approach to Force-Field Calibration.

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 f

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

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

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

An efficient molecular docking using conformational space annealing

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

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

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

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

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

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

Charge loss in gas-phase multiply negatively charged oligonucleotides

Coarse-Grained Models of Proteins: Theory and Applications

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

Computational techniques for efficient conformational sampling of proteins

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

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

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

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

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

Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes

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

Dynamics study on single and multiple β-sheets

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

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

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

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

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

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

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

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

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

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.

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

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.

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

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

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

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

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

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.

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

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

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.

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

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

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

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

Molecular modeling of the human vasopressin V2 receptor/agonist complex

Molecular origin of anticooperativity in hydrophobic association

Molecular simulation study of cooperativity in hydrophobic association

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

Molecular simulations of rhodopsin tetrameter.

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

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models

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

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

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

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

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

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

Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations

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

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

Potential of mean force of hydrophobic association: dependence on solute size.

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

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

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

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

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

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

Recent Developments in Data-Assisted Modeling of Flexible Proteins

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

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

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

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

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. 3. Calculation and Parameterization of the Potentials of Mean Force of Pairs of Identical Hydrophobic Side Chains