Filtros de búsqueda

Lista de obras de Jaroslav Koča

A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase. 2. Quantum Chemical Study of Complete Reaction Mechanism

article by Michal Kutý et al published July 1998 in Journal of Chemical Information and Computer Sciences

A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase:  1. Quantum Chemical Study of the First Reaction Step

article by Jiří Damborský et al published May 1997 in Journal of Chemical Information and Computer Sciences

A QM/MM investigation of the catalytic mechanism of metal-ion-independent core 2 β1,6-N-acetylglucosaminyltransferase

artículo científico publicado en 2013

A combination of driving method with simulated annealing to search conformational space

A mathematical model of the logical structure of chemistry. A bridge between theoretical and experimental chemistry and a general tool for computer-assisted molecular design

A mathematical model of the logical structure of chemistry. A bridge between theoretical and experimental chemistry and a general tool for computer-assisted molecular design

A novel mechanism of proton transfer in protonated peptides

artículo científico publicado en 2003

A-like guanine-guanine stacking in the aqueous DNA duplex of d(GGGGCCCC).

artículo científico publicado en 2001

Abstract 3084: MicroRNA involvement in DNA damage response and BCR signaling in malignant B cells

Abstract 5198: Identification of microRNAs involved in DNA damage response in malignant B cells and their biological and clinical relevance

Acetylcholinesterases--the structural similarities and differences

artículo científico publicado en 2007

Activation and inhibition of cyclin-dependent kinase-2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine-rich loop

artículo científico publicado en 2004

An A-type double helix of DNA having B-type puckering of the deoxyribose rings.

artículo científico publicado en 2000

Analysis of CDK2 active-site hydration: a method to design new inhibitors

artículo científico publicado en 2004

Analysis of the reaction mechanism and substrate specificity of haloalkane dehalogenases by sequential and structural comparisons

artículo científico publicado en 1999

Anatomy of enzyme channels

artículo científico publicado en 2014

Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions

scientific article published on 15 August 2018

Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges

artículo científico publicado en 2020

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules

artículo científico publicado en 2015

Automated Family-Wide Annotation of Secondary Structure Elements

artículo científico publicado en 2019

Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions

artículo científico publicado en 2017

Behavior of BsoBI endonuclease in the presence and absence of DNA.

artículo científico publicado en 2017

BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management

artículo científico publicado en 2020

Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops

article

Biomacromolecular Fragments and Patterns

Channel Characteristics

ChannelsDB: database of biomacromolecular tunnels and pores

artículo científico publicado en 2017

Characterization via Charges

Charge profile analysis reveals that activation of pro-apoptotic regulators Bax and Bak relies on charge transfer mediated allosteric regulation

artículo científico publicado en 2012

Comparison of force-fields parametrizations as applied to conformational analysis of ribofuranosides

Complete Process of Data Extraction and Analysis

Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods

scientific article published in 2004

Computational Studies on the Stability of [Amide]Br-Complexes†

Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models

Computational site-directed mutagenesis of haloalkane dehalogenase in position 172.

artículo científico publicado en 1998

Computer Modeling and Simulations on Flexible Bifunctional Systems: Intramolecular Energy Transfer Implications†

Computer simulation of histo-blood group oligosaccharides: energy maps of all constituting disaccharides and potential energy surfaces of 14 ABH and Lewis carbohydrate antigens

artículo científico publicado en 1995

Concluding Remarks

Conformational analysis and flexibility of carbohydrates using the CICADA approach with MM3

article

Conformational analysis of complex oligosaccharides: the CICADA approach to the uromodulin O-glycans

artículo científico publicado en 2004

Conformational behavior and flexibility of terminally blocked alanine di- and tripeptides

Conformational behavior of insect pheromones and analogues. Part II

article by Jaroslav Koča & Per H.J. Carlsen published April 1992 in Journal of Molecular Structure

Conformational behavior of pheromones and analogues Part I. 3-methyl-2-buten-1-ol, 3,3,6-trimethyl-1, 5- heptadien-4-ol and 2-methyl-6-methylene-2,7-octadien-4- on

Conformational flexibility of two RNA trimers explored by computational tools and database search

artículo científico publicado en 2003

Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics

artículo científico publicado en 2007

Consistency of sugar structures and their annotation in the PDB.

artículo científico publicado en 2014

Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics

artículo científico publicado en 2003

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing

artículo científico publicado en 2017

Detection and Extraction of Fragments

Detection of Channels

Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2.

artículo científico publicado en 2016

Different mechanisms of CDK5 and CDK2 activation as revealed by CDK5/p25 and CDK2/cyclin A dynamics

artículo científico publicado en 2006

Dispersion interactions of carbohydrates with condensate aromatic moieties: Theoretical study on the CH–π interaction additive properties

artículo científico publicado en 2011

Docking-Based Development of Purine-like Inhibitors of Cyclin-Dependent Kinase-2

artículo científico publicado en 2000

Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations

artículo científico publicado en 2002

Effect of Cation Concentration on Molecular Dynamics Simulations of UDP-Glucose

article

Effect of solvation on pinched cone-pinched cone interconversion of tetraethoxycalix[4]arene and tetraethoxythiacalix[4]arene

artículo científico publicado en 2006

Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA

artículo científico publicado en 2007

Electronegativity Equalization Method: Parameterization and Validation for Large Sets of Organic, Organohalogene and Organometal Molecule.

artículo científico publicado en 2007

Empirical charges for chemoinformatics applications.

artículo científico publicado en 2014

Enantioselective chromatography and molecular modeling of novel aryloxyaminopropan-2-ols with the alkyl carbamate function

artículo científico publicado en 2004

Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity.

artículo científico publicado en 2014

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation

article published in 2013

Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes

artículo científico publicado en 2015

Exercises Solution

Exploring reaction pathways for O-GlcNAc transferase catalysis. A string method study

artículo científico publicado en 2015

Extended molecular dynamics of a c-kit promoter quadruplex

artículo científico publicado en 2015

Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates

artículo científico publicado en 2003

Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation

artículo científico publicado en 2007

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

artículo científico publicado en 2015

Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis

artículo científico publicado en 2002

High affinity fucose binding of Pseudomonas aeruginosa lectin PA-IIL: 1.0 A resolution crystal structure of the complex combined with thermodynamics and computational chemistry approaches

artículo científico publicado en 2005

High-performance macromolecular data delivery and visualization for the web

artículo científico publicado en 2020

High-performance macromolecular data delivery and visualization for the web. Corrigendum

artículo científico publicado en 2021

High-quality and universal empirical atomic charges for chemoinformatics applications

artículo científico publicado en 2015

Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases

artículo científico publicado en 2005

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction?

scientific article published on 11 June 2015

How Mycobacterium tuberculosis Galactofuranosyl Transferase 2 (GlfT2) Generates Alternating β-(1-6) and β-(1-5) Linkages: A QM/MM Molecular Dynamics Study of the Chemical Steps.

artículo científico publicado en 2018

How ionic strength affects the conformational behavior of human and rat beta amyloids--a computational study

artículo científico publicado en 2013

How the methodology of 3D structure preparation influences the quality of QSPR models?

artículo científico publicado en 2012

Importance of oligomerisation on Pseudomonas aeruginosaLectin-II binding affinity. In silico and in vitro mutagenesis

artículo científico publicado en 2009

In Silico Engineering of Proteins That Recognize Small Molecules

In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding

scientific article published on 11 May 2012

In silico mutagenesis and docking studies of Pseudomonas aeruginosa PA-IIL lectin predicting binding modes and energies

artículo científico publicado en 2008

Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL.

artículo científico publicado en 2017

Influence of stereochemistry on proton transfer in protonated tripeptide models

Influence of the Acetylcholinesterase Active Site Protonation on Omega Loop and Active Site Dynamics ⬇️

artículo científico publicado el 1 de diciembre de 2010

Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic ¹⁵N chemical shielding anisotropy tensors

artículo científico publicado en 2012

Interactions of amyloid β peptide 1-40 and cerebrosterol.

artículo científico publicado en 2011

Introduction

Investigation of the complexation of (+)-catechin by beta-cyclodextrin by a combination of NMR, microcalorimetry and molecular modeling techniques

artículo científico publicado en 2003

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

artículo científico publicado en 2014

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data

artículo científico publicado en 2017

Long-range electrostatic interactions in molecular dynamics: an endothelin-1 case study

artículo científico publicado en 2005

Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex

artículo científico publicado en 2004

MAPOS: a computer program for organic synthesis design based on synthon model of organic chemistry

artículo científico publicado en 1991

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

artículo científico publicado en 2013

MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels

artículo científico publicado en 2007

MOLECULAR ORBITAL CALCULATIONS TO DESCRIBE MICROBIAL REDUCTIVE DECHLORINATION OF POLYCHLORINATED DIOXINS

artículo científico publicado en 1998

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

artículo científico publicado en 2012

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).

artículo científico publicado en 2018

Mechanism of Proton Transfer in Short Protonated Oligopeptides. 1.N-Methylacetamide andN2-Acetyl-N1-methylglycinamide

Mechanism of hydrogen-bond array isomerization in tetrahydroxycalix[4]arene and tetrahydroxythiacalix[4]arene

artículo científico publicado en 2008

Mobility of the active site bound paraoxon and sarin in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation

artículo científico publicado en 2001

Mole 2.5 - Tool for Detection and Analysis of Macromolecular Pores and Channels

scholarly article by Karel Berka et al published February 2017 in Biophysical Journal

Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease

artículo científico publicado en 2014

Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations

artículo científico publicado en 2004

Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets

artículo científico publicado en 2003

Molecular dynamics simulations of glycosyltransferase LgtC.

artículo científico

Molecular dynamics simulations of solvated UDP-glucose in interaction with Mg2+ cations

artículo científico publicado en 2001

Molecular dynamics study of Pseudomonas aeruginosa lectin-II complexed with monosaccharides

artículo científico publicado en 2008

Molecular modeling of glycosyltransferases

artículo científico publicado en 2006

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes

artículo científico publicado en 2014

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges

artículo científico publicado en 2016

Nemesis - a molecular modeling package.

artículo científico publicado en 2013

Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

artículo científico publicado en 2003

Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method

artículo científico publicado en 2006

PDBe: improved findability of macromolecular structure data in the PDB

artículo científico publicado en 2020

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank

artículo científico publicado en 2015

Potential Energy Hypersurfaces of Nucleotide Sugars: Ab Initio Calculations, Force-Field Parametrization, and Exploration of the Flexibility

scientific article published in 1999

Potential energy hypersurface and molecular flexibility

Predicting non-sentinel lymph node status after positive sentinel biopsy in breast cancer: what model performs the best in a Czech population?

artículo científico publicado en 2009

Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes

artículo científico publicado en 2011

Predicting pKa values from EEM atomic charges

artículo científico publicado en 2013

Protein engineering study of β-mannosidase to set up a potential chemically efficient biocatalyst.

artículo científico publicado en 2014

QM quality atomic charges for proteins.

artículo científico publicado en 2014

QSPR designer – employ your own descriptors in the automated QSAR modeling process.

artículo científico publicado en 2012

Quantum-Chemical Insight Into Mechanism of Combined Intra-Intermolecular Cycloaddition

RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics

article

Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method

artículo científico publicado en 2013

Reactions graphs

article

Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations

artículo científico publicado en 2010

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

artículo científico publicado en 2012

Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations

artículo científico publicado en 2008

Repositioning the catalytic triad aspartic acid of haloalkane dehalogenase: effects on stability, kinetics, and structure.

artículo científico publicado en 1997

Ribosomal RNA Kink-turn Motif—A Flexible Molecular Hinge

artículo científico publicado en 2004

Searching for tunnels of proteins – comparison of approaches and available software tools.

artículo científico publicado en 2012

Selectins-The Two Dr. Jekyll and Mr. Hyde Faces of Adhesion Molecules-A Review

artículo científico publicado en 2020

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

artículo científico publicado en 2009

Single-Coordinate-Driving Method Coupled with Simulated Annealing.An Efficient Tool To Search Conformational Space

article

Single-coordinate-driving method for molecular docking: application to modeling of guest inclusion in cyclodextrin.

artículo científico publicado en 2000

SiteBinder – an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs.

artículo científico publicado en 2012

SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs

scientific database

Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme

article

Stability of Complexes of Aromatic Amides with Bromide Anion:  Quantitative Structure−Property Relationships

article

Stacking interactions between carbohydrate and protein quantified by combination of theoretical and experimental methods

artículo científico publicado en 2012

Stepwise catalytic mechanism via short-lived intermediate inferred from combined QM/MM MERP and PES calculations on retaining glycosyltransferase ppGalNAcT2

artículo científico publicado en 2015

Structural Bioinformatics Databases of General Use

Structural Bioinformatics Tools for Drug Design

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

artículo científico publicado en 2013

Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations

artículo científico publicado en 2006

Structures and mechanisms of glycosyltransferases

artículo científico publicado en 2005

Substrate-Assisted Catalytic Mechanism of O-GlcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation

artículo científico publicado en 2012

TRITON: a graphical tool for ligand-binding protein engineering

artículo científico publicado en 2008

TRITON: graphic software for rational engineering of enzymes.

artículo científico publicado en 2001

TRITON: in silico construction of protein mutants and prediction of their activities

artículo científico publicado en 2000

The CH-π interaction in protein - carbohydrate binding: Bioinformatics and in vitro quantification

scientific article published on 24 March 2020

The Eighth Central European Conference "Chemistry towards Biology": Snapshot

artículo científico publicado en 2016

The conformational behaviour of thiacalix[4]arenes: the pinched cone–pinched cone transition

article

The mechanism of inhibition of the cyclin-dependent kinase-2 as revealed by the molecular dynamics study on the complex CDK2 with the peptide substrate HHASPRK

artículo científico publicado en 2005

The structure and dynamics of chitin nanofibrils in an aqueous environment revealed by molecular dynamics simulations

article

Three-dimensional homology model of GlcNAc-TV glycosyltransferase

artículo científico

Three-dimensional potential energy surface of selected carbohydrates' CH/π dispersion interactions calculated by high-level quantum mechanical methods

artículo científico publicado en 2011

Travelling on the potential energy surfaces of carbohydrates: comparative application of an exhaustive systematic conformational search with an heuristic search

artículo científico publicado en 1995

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

article

Unrestrained Molecular Dynamics Simulations of [d(AT)5]2Duplex in Aqueous Solution: Hydration and Binding of Sodium Ions in the Minor Groove

article

VADER:  New Software for Exploring Interconversions on Potential Energy Surfaces†

scholarly article by Martin Černohorský et al published July 1999 in Journal of Chemical Information and Computer Sciences

ValTrendsDB: bringing Protein Data Bank validation information closer to the user

scientific article published on 01 December 2019

Validation

book chapter in Structural Bioinformatics Tools for Drug Design (2016)

Validation of two conformational searching methods applied to sucrose: simulation of NMR and chiro-optical data

article published in 1997

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank

artículo científico publicado en 2015

Virtual screening and in silico design of novel inhibitors of bacterial lectins.

artículo científico publicado en 2012

Visualization and Analysis of Protein Structures with LiteMol Suite

artículo científico publicado en 2020

Why acetylcholinesterase reactivators do not work in butyrylcholinesterase

artículo científico publicado en 2010

Dominio Público Uruguay está sostenido por:

Acerca de Dominio Público Uruguay

Ayuda