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 1995
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Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
Publikacja
Rok 1996
Rok 1997
Rok 1998
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Computer modeling of the solution conformation of cyclic enkephalins
Publikacja -
Vasopressin V2 receptor/bioligand interactions
Publikacja
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?
Publikacja -
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 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
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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 -
Solution conformational study of Scyliorhinin I analogues with conformational constraints by two-dimensional NMR and theoretical conformational analysis
Publikacja
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
Publikacja -
Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes
Publikacja -
Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing
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Recent improvements in prediction of protein structure by global optimization of a potential energy function
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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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The investigation of the effects of counterions in protein dynamics simulations
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?
Publikacja -
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)]
Publikacja -
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
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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
Publikacja
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 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]
Publikacja -
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
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The protein folding problem: global optimization of force fields
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Towards gelsolin amyloid formation
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Use of NMR and Fluorescence Spectroscopy as well as Theoretical Conformational Analysis in Conformation-activity Studies of Cyclic Enkephalin Analogues
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
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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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Reply to “Comment on ‘Molecular Origin of Anticooperativity in Hydrophobic Association'”
Publikacja
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
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Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES) Force Field
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The Protein Folding Problem
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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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
Publikacja
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
Publikacja -
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
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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
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Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
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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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
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
Publikacja -
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
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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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Theoretical Study of Polymerization Mechanism of p-Xylylene Based Polymers
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Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations
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 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
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Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics
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 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
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Rapid communication: Computational simulation and analysis of a candidate for the design of a novel silk-based biopolymer
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Solvatochromic studies of pull–push molecules containing dimethylaniline and aromatic hydrocarbon linked by an acetylene unit
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
Publikacja
wyświetlono 530 razy