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 1998
Rok 2018
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Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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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 2016
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Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field
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Temperature-dependent structure-property modeling of viscosity for ionic liquids
PublikacjaIn 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...
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Photophysical properties of symmetrically substituted diarylacetylenes and diarylbuta-1,3-diynes
Publikacja
Rok 2004
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Use of NMR and Fluorescence Spectroscopy as well as Theoretical Conformational Analysis in Conformation-activity Studies of Cyclic Enkephalin Analogues
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Towards gelsolin amyloid formation
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The protein folding problem: global optimization of force fields
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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 2023
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UNRES-GPU for Physics-Based Coarse-Grained Simulations of Protein Systems at Biological Time- and Size-Scales
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 2021
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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
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Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
Publikacja
Rok 2009
Rok 2010
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Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations
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Theoretical Study of Polymerization Mechanism of p-Xylylene Based Polymers
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Theoretical study of polymerization mechanism of p-xylylene based polymers
PublikacjaObliczenia kwantowe mechanizmu polimeryzacji parylenów, opartych o cząsteczki p-ksylilenów. Praca zawiera wyniki szczegółowych obliczeń wszystkich etapów polimeryzacji, wnioski dotyczące znalezionych stanów kwantowych i energetyki poszczególnych etapów procesu.
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Potential of Mean Force of Association of Large Hydrophobic Particles: Toward the Nanoscale Limit
Publikacja
Rok 2022
Rok 2017
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Theoretical calculation of the physico-chemical properties of 1-butyl-4-methylpyridinium based ionic liquids
PublikacjaACCEPTED 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...
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Role of the sulfur to α-carbon thioether bridges in thurincin H
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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...
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Photophysical and theoretical studies of diphenylacetylene derivatives with restricted rotation
Publikacja
Rok 2006
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The Protein Folding Problem
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Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES) Force Field
Publikacja
Rok 1996
Rok 2001
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The investigation of the effects of counterions in protein dynamics simulations
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Synthesis, activity on NK-3 tachykinin receptor and conformational solution studies of scyliorhinin II analogs modified at position 16
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Recent improvements in prediction of protein structure by global optimization of a potential energy function
Publikacja
Rok 1995
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Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
Publikacja
Rok 2014
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Solvatochromic studies of pull–push molecules containing dimethylaniline and aromatic hydrocarbon linked by an acetylene unit
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Rapid communication: Computational simulation and analysis of a candidate for the design of a novel silk-based biopolymer
Publikacja
Rok 2000
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Solution conformational study of Scyliorhinin I analogues with conformational constraints by two-dimensional NMR and theoretical conformational analysis
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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
Publikacja
Rok 2012
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Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics
Publikacja
Rok 2008
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Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
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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
Publikacja
Rok 2007
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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
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Potential of Mean Force of Hydrophobic Association: Dependence on Solute Size
Publikacja
Rok 2020
Rok 2005
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Reply to “Comment on ‘Molecular Origin of Anticooperativity in Hydrophobic Association'”
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Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC
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Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests
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Rok 2002
Rok 2019
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Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis
Publikacja
Rok 1999
Rok 2015
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Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field
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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
Publikacja
Rok 2013
wyświetlono 530 razy