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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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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1,4-DHP-lipid parameters and rod like micellae
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Dynamics study on single and multiple β-sheets
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Chemoinformatics Methods for Studying Biomolecules
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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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Lipid-protein interactions in membranes: a molecular modelling study
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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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Extension of the Force Matching Method to Anisotropic Coarse-Grained Transferable Force Fields: Application to the Unres Model of Proteins
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1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins
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Molecular Modelling of the Neurophysin II/Vasopressin Complex
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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 dynamics simulation of polymerization of p-xylylene
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Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
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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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Reply to “Comment on ‘Molecular Origin of Anticooperativity in Hydrophobic Association'”
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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 Protein Folding Problem
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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...
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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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Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
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Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations
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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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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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Theoretical Investigation of the Coronavirus SARS-CoV-2 (COVID-19) Infection Mechanism and Selectivity
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Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems
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Vasopressin V2 receptor/bioligand interactions
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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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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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Meta-computations on the CLUSTERIX Grid
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Comment on “Molecular Origin of Anticooperativity in Hydrophobic Association”
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Molecular Simulations of Rhodopsin Tetrameter
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Multiple β-sheet molecular dynamics of amyloid formation from two ABl-SH3 domain peptides
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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...
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Deltorphin analogs restricted via a urea bridge: structure and opioid activity
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Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models
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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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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
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Molecular dynamics study of amyloid formation of two Abl-SH3 domain peptides
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Molecular dynamics simulations of the growth of poly(chloro-para-xylylene) films
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Common functionally important motions of the nucleotide‐binding domain of H sp70
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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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Conformation-activity relationships ofcyclo-constrained µ/δ opioid agonists derived from theN-terminal tetrapeptide segment of dermorphin/deltorphin
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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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Charge Loss in Gas-Phase Multiply Negatively Charged Oligonucleotides
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Computer modeling of the solution conformation of cyclic enkephalins
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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
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Photophysical and theoretical studies of diphenylacetylene derivatives with restricted rotation
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Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field
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Towards gelsolin amyloid formation
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Molecular Dynamics of a Vasopressin V2 Receptor in a Phospholipid Bilayer Membrane
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Role of the sulfur to α-carbon thioether bridges in thurincin H
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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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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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Conformational studies of cyclic enkephalin analogues withL- orD-proline in position 3
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The photophysics of β-homo-tyrosine and its simple derivatives
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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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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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Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
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Global Optimization-Based Method for Deriving Intermolecular Potential Parameters for Crystals
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Experimental and theoretical studies of spectroscopic properties of simple symmetrically substituted diphenylbuta-1,3-diyne derivatives
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Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
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Coarse-Grained Models of Proteins: Theory and Applications
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Bladder cancer detection using a peptide substrate of the 20S proteasome
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Photophysical properties of symmetrically substituted diarylacetylenes and diarylbuta-1,3-diynes
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Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis
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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
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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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Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field
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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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Conformational studies of vasopressin and mesotocin using NMR spectroscopy and molecular modelling methods. Part II: studies in the SDS micelle
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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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Solvatochromic studies of pull–push molecules containing dimethylaniline and aromatic hydrocarbon linked by an acetylene unit
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Photophysical properties of 3-[2-(N-phenylcarbazolyl)benzoxazol-5-yl]alanine derivatives – experimental and theoretical studies
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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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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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Deltorphin analogs restricted via a urea bridge: structure and opioid activity
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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
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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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Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
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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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Evolution of physics-based methodology for exploring the conformational energy landscape of proteins
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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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Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
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The investigation of the effects of counterions in protein dynamics simulations
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Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods
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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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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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Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
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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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Molecular Origin of Anticooperativity in Hydrophobic Association
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Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles
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Theoretical Study of Polymerization Mechanism of p-Xylylene Based Polymers
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An efficient molecular docking using conformational space annealing
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Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
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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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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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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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wyświetlono 530 razy