prof. dr hab. Cezary Czaplewski
Zatrudnienie
- 2017 - 2021 assistant professor (part-time) w Wydział Fizyki Technicznej i Matematyki Stosowanej
Publikacje
Filtry
wszystkich: 137
Katalog Publikacji
Rok 2012
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1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins
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Molecular dynamics simulation of polymerization of p-xylylene
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Multiple β-sheet molecular dynamics of amyloid formation from two ABl-SH3 domain peptides
Publikacja
Rok 2011
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1,4-DHP-lipid parameters and rod like micellae
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Coarse-Grained Models of Proteins: Theory and Applications
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Molecular dynamics simulations of the growth of poly (chloro-para-xylylene) films.
PublikacjaParylene C, poly(chloro-para-xylylene) is the most widely used member of the parylene family due to its excellent chemical and physical properties. In this work we analyzed the formation of the parylene C film using molecular mechanics and molecular dynamics methods. A five unit chain is necessary to create a stable hydrophobic cluster and to adhere to a covered surface. Two scenarios were deemed to take place. The obtained results...
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Molecular dynamics simulations of the growth of poly(chloro-para-xylylene) films
Publikacja
Rok 2010
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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
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Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
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Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field
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Potential of Mean Force of Association of Large Hydrophobic Particles: Toward the Nanoscale Limit
Publikacja
Rok 2019
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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
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Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
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Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
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Extension of the Force Matching Method to Anisotropic Coarse-Grained Transferable Force Fields: Application to the Unres Model of Proteins
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Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
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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
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Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis
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Rok 2006
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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
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Molecular dynamics study of amyloid formation of two Abl-SH3 domain peptides
Publikacja
Rok 2015
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A Maximum-Likelihood Approach to Force-Field Calibration
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Common functionally important motions of the nucleotide‐binding domain of H sp70
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Experimental and theoretical studies of spectroscopic properties of simple symmetrically substituted diphenylbuta-1,3-diyne derivatives
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Experimental and theoretical studies of the spectroscopic properties of simple symmetrically substituted diphenylacetylene derivatives
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Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations
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Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field
Publikacja
Rok 2002
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A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field
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Can cooperativity in hydrophobic association be reproduced correctly by implicit solvation models?
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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)]
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Conformational studies of cyclic enkephalin analogues withL- orD-proline in position 3
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Evolution of physics-based methodology for exploring the conformational energy landscape of proteins
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Lipid-protein interactions in membranes: a molecular modelling study
Publikacja
Rok 2014
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A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
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Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements
Publikacja
Rok 2018
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Acid-base properties of 3-[2-(n-quinolinyl)benzoxazol-5-yl]alanine derivatives in the ground and excited state. Experimental and theoretical studies
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An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
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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
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Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
Publikacja
Rok 2013
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Acid–base properties of 3-[2-(pyridyl)benzoxazol-5-yl]alanine derivatives in the ground and excited state. Experimental and theoretical studies
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Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States
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Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
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Photophysical properties of 3-[2-(N-phenylcarbazolyl)benzoxazol-5-yl]alanine derivatives – experimental and theoretical studies
Publikacja
Rok 2005
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An efficient molecular docking using conformational space annealing
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Charge Loss in Gas-Phase Multiply Negatively Charged Oligonucleotides
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Comment on “Molecular Origin of Anticooperativity in Hydrophobic Association”
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Comparison of two approaches to potential of mean force calculations of hydrophobic association: particle insertion and weighted histogram analysis methods
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Molecular Origin of Anticooperativity in Hydrophobic Association
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Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests
Publikacja
Rok 2009
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Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
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Conformation-activity relationships of cyclo-constrained μ/5 opioid agonists derived from the N-terminal tetrapeptide segment of dermorphin/deltorphin
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Deltorphin analogs restricted via a urea bridge: structure and opioid activity
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Dynamics study on single and multiple β-sheets
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Rok 1999
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Binding modes of a new epoxysuccinyl–peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity?
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Molecular Dynamics of a Vasopressin V2 Receptor in a Phospholipid Bilayer Membrane
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Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods
Publikacja
Rok 2016
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Bladder cancer detection using a peptide substrate of the 20S proteasome
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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
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Photophysical properties of symmetrically substituted diarylacetylenes and diarylbuta-1,3-diynes
Publikacja
Rok 2017
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Chemoinformatics Methods for Studying Biomolecules
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Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
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Photophysical and theoretical studies of diphenylacetylene derivatives with restricted rotation
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Polymerization of chloro-p-xylylenes, quantum-chemical study
PublikacjaThe 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...
Rok 2008
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Computational techniques for efficient conformational sampling of proteins
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Conformation-activity relationships ofcyclo-constrained µ/δ opioid agonists derived from theN-terminal tetrapeptide segment of dermorphin/deltorphin
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Conformational studies of vasopressin and mesotocin using NMR spectroscopy and molecular modelling methods. Part II: studies in the SDS micelle
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Deltorphin analogs restricted via a urea bridge: structure and opioid activity
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Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field
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Implementations of Nosé–Hoover and Nosé–Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain
Publikacja
Rok 1998
Rok 2001
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Conformation-family Monte Carlo: A new method for crystal structure prediction
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Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field
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Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes
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Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing
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Rok 2000
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Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions
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Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals
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Molecular simulation study of cooperativity in hydrophobic association
Publikacja
Rok 2007
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field
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Meta-computations on the CLUSTERIX Grid
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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
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Molecular Simulations of Rhodopsin Tetrameter
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Potential of Mean Force of Hydrophobic Association: Dependence on Solute Size
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Rok 2004
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Erratum to “Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles” [Biophys. Chem. 105 (2003) 339–359]
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Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 3. Use of Many Proteins in Optimization
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Parametrization of Backbone−Electrostatic and Multibody Contributions to the UNRES Force Field for Protein-Structure Prediction from Ab Initio Energy Surfaces of Model Systems
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Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds
Publikacja
Rok 2020
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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
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Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models
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Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
Publikacja
Rok 2021
Rok 2003
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Global Optimization-Based Method for Deriving Intermolecular Potential Parameters for Crystals
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Molecular dynamics study of a gelsolin-derived peptide binding to a lipid bilayer containing phosphatidylinositol 4,5-bisphosphate
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Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain
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Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles
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Molecular Simulation Study of the Potentials of Mean Force for the Interactions between Models of Like-Charged and between Charged and Nonpolar Amino Acid Side Chains in Water
Publikacja
Rok 2023
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Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
PublikacjaThe 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...
Rok 1997
wyświetlono 530 razy