Search
prof. dr hab. Cezary Czaplewski
Employment
- 2017 - 2021 assistant professor (part-time) at Faculty of Applied Physics and Mathematics
Publications
Filters
total: 138
Catalog Publications
Year 2024
-
Multi-GPU-powered UNRES package for physics-based coarse-grained simulations of structure, dynamics, and thermodynamics of protein systems at biological size- and timescales
PublicationCoarse-grained models are nowadays extensively used in biomolecular simulations owing to the tremendous extension of size- and time-scale of simulations. The physics-based UNRES (UNited RESidue) model of proteins developed in our laboratory has only two interaction sites per amino-acid residue (united peptide groups and united side chains) and implicit solvent. However, owing to rigorous physics-based derivation, which enabled...
Year 2023
-
Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
-
UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
PublicationThe dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that...
Year 2022
-
Theoretical Investigation of the Coronavirus SARS-CoV-2 (COVID-19) Infection Mechanism and Selectivity
Publication
Year 2021
-
Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems
Publication -
Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
Publication -
UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
Publication
Year 2020
-
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
Publication -
Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models
Publication -
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
Publication -
Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
Publication
Year 2019
-
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
Publication -
Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
Publication -
Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
Publication -
Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
Publication -
Extension of the Force Matching Method to Anisotropic Coarse-Grained Transferable Force Fields: Application to the Unres Model of Proteins
Publication -
Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
Publication -
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
Publication -
Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis
Publication
Year 2018
-
Acid-base properties of 3-[2-(n-quinolinyl)benzoxazol-5-yl]alanine derivatives in the ground and excited state. Experimental and theoretical studies
Publication -
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
Publication -
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
Publication -
Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
Publication -
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
Publication -
Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets
Publication
Year 2017
-
Chemoinformatics Methods for Studying Biomolecules
Publication -
Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
Publication -
Photophysical and theoretical studies of diphenylacetylene derivatives with restricted rotation
Publication -
Polymerization of chloro-p-xylylenes, quantum-chemical study
PublicationThe p-xylylene monomers of parylene N, C and D have similar high polymerization reactivity. For effective copolymerization processes this fact is basically a draw- back and for instance the copolymerization with styrene doesn't go at all (Corley et al. J Pol Sc 13(68):137156, 1954). Substitution of terminal hydrogen atoms by chlorine atoms reduces reactivity dramatically. 7,7,8,8-tetrachloro-p- xylylene and 2,5,7,7,8,8-hexachloro-p-xylylene...
-
Role of the sulfur to α-carbon thioether bridges in thurincin H
Publication -
Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids
PublicationACCEPTED MAIonic liquids (ILs) have attracted much attention for their unique physicochemical properties, which can be designed as needed by altering the ion combinations. Besides experimental work, numerous computational studies have been concerned with prediction of physical properties of ILs. The results of molecular dynamics simulations of ILs depend strongly on the proper force field parameterization. Classical force fields...
Year 2016
-
Bladder cancer detection using a peptide substrate of the 20S proteasome
Publication -
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
Publication -
Photophysical properties of symmetrically substituted diarylacetylenes and diarylbuta-1,3-diynes
Publication -
Temperature-dependent structure-property modeling of viscosity for ionic liquids
PublicationIn this paper we present the methodology for assessing the ionic liquids' viscosity at six temperature points (25, 35, 45, 50, 60 and 70 [C]), which utilizes only the in silico approach. The main idea of such assessment is based on the "correction equation" describing the correlation between experimentally measured viscosity and theoretically derived density (calculated with use of molecular mechanics), given at 6 different temperature...
-
Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field
Publication
Year 2015
-
A Maximum-Likelihood Approach to Force-Field Calibration
Publication -
Common functionally important motions of the nucleotide‐binding domain of H sp70
Publication -
Experimental and theoretical studies of spectroscopic properties of simple symmetrically substituted diphenylbuta-1,3-diyne derivatives
Publication -
Experimental and theoretical studies of the spectroscopic properties of simple symmetrically substituted diphenylacetylene derivatives
Publication -
Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations
Publication -
Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field
Publication
Year 2014
-
A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
Publication -
Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements
Publication -
Rapid communication: Computational simulation and analysis of a candidate for the design of a novel silk-based biopolymer
Publication -
Solvatochromic studies of pull–push molecules containing dimethylaniline and aromatic hydrocarbon linked by an acetylene unit
Publication
Year 2013
-
Acid–base properties of 3-[2-(pyridyl)benzoxazol-5-yl]alanine derivatives in the ground and excited state. Experimental and theoretical studies
Publication -
Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States
Publication -
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
Publication -
Photophysical properties of 3-[2-(N-phenylcarbazolyl)benzoxazol-5-yl]alanine derivatives – experimental and theoretical studies
Publication
seen 1391 times