Wyszukiwarka
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
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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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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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Recent improvements in prediction of protein structure by global optimization of a potential energy function
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Computational techniques for efficient conformational sampling of proteins
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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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A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
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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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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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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
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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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Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field
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Molecular simulation study of cooperativity in hydrophobic association
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Potential of Mean Force of Association of Large Hydrophobic Particles: Toward the Nanoscale Limit
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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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Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
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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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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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Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES) Force Field
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Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics
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Potential of Mean Force of Hydrophobic Association: Dependence on Solute Size
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Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing
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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
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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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Conformation-family Monte Carlo: A new method for crystal structure prediction
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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field
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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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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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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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Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals
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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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Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements
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Can cooperativity in hydrophobic association be reproduced correctly by implicit solvation models?
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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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The protein folding problem: global optimization of force fields
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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
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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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Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds
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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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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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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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Experimental and theoretical studies of the spectroscopic properties of simple symmetrically substituted diphenylacetylene derivatives
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A Maximum-Likelihood Approach to Force-Field Calibration
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Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
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An efficient molecular docking using conformational space annealing
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Theoretical Study of Polymerization Mechanism of p-Xylylene Based Polymers
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Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles
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Molecular Origin of Anticooperativity in Hydrophobic Association
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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
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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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wyświetlono 530 razy