List of works - 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

scientific article published on 24 April 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 novel mechanism of proton transfer in protonated peptides

scientific article published in November 2003

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

scientific article

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

scientific article published in August 2007

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

scientific article published on 7 May 2004

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

scientific article

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

scientific article published in May 2004

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

scientific article

Anatomy of enzyme channels

scientific article

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

scientific article published on 13 May 2020

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

scientific article (publication date: 2015)

Automated Family-Wide Annotation of Secondary Structure Elements

scientific article published on 01 January 2019

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

scientific article

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

scientific article published on 20 December 2017

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

scientific article published on 19 October 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

scientific article published on 3 October 2017

Characterization via Charges

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

scientific article

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.

scientific article

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

scientific article published on 01 June 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

scientific article published in April 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

scientific article published in April 2003

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

scientific article

Consistency of sugar structures and their annotation in the PDB.

scientific article published on 11 March 2014

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

scientific article

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

scientific article published on 24 July 2017

Detection and Extraction of Fragments

Detection of Channels

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

scientific article

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

scientific article published on 9 January 2006

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

scientific article published on 14 July 2011

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

article

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

scientific article published in October 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

scientific article published in January 2006

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

scientific article published on 6 June 2007

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

scientific article published on 3 July 2007

Empirical charges for chemoinformatics applications.

scientific article published on 11 March 2014

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

scientific article published in March 2004

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

scientific article

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

scientific article published on 2 July 2015

Exercises Solution

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

scientific article published on 17 March 2015

Extended molecular dynamics of a c-kit promoter quadruplex

scientific article

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

scientific article

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

scientific article

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

scientific article published on 3 October 2015

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

scientific article

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

scientific article

High-performance macromolecular data delivery and visualization for the web

scientific article published on 26 November 2020

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

scientific article published on 01 January 2021

High-quality and universal empirical atomic charges for chemoinformatics applications

scientific article (publication date: 2015)

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

scientific article

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.

scientific article published on 25 March 2018

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

scientific article

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

scientific article

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

scientific article published on 11 March 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

scientific article published on November 2008

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

scientific article published on 12 December 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 ⬇️

scientific article published on December 1, 2010

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

scientific article published in December 2012

Interactions of amyloid β peptide 1-40 and cerebrosterol.

scientific article published on 17 November 2011

Introduction

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

scientific article

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

scientific article published on 01 March 2014

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

scientific article published in November 2017

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

scientific article published on 01 October 2005

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

scientific article

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

scientific article published in August 1991

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

scientific article (publication date: 16 August 2013)

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

scientific article published in November 2007

MOLECULAR ORBITAL CALCULATIONS TO DESCRIBE MICROBIAL REDUCTIVE DECHLORINATION OF POLYCHLORINATED DIOXINS

scientific article published in 1998

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

scientific article

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

scientific article published in July 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

scientific article published on 9 January 2008

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

scientific article published in February 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

scientific article published on 24 October 2014

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

scientific article

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

scientific article

Molecular dynamics simulations of glycosyltransferase LgtC.

scientific article published on April 2004

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

scientific article

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

scientific article published in July 2008

Molecular modeling of glycosyltransferases

scientific article published on January 2006

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

scientific article

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

scientific article (publication date: 2016)

Nemesis - a molecular modeling package.

scientific article published on 22 March 2013

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

scientific article

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

scientific article published in February 2006

PDBe: improved findability of macromolecular structure data in the PDB

scientific article published on 01 January 2020

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

scientific article

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?

scientific article published on 15 May 2009

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

scientific article published in August 2011

Predicting pKa values from EEM atomic charges

scientific article published on 10 April 2013

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

scientific article published on 21 July 2014

QM quality atomic charges for proteins.

scientific article published on 11 March 2014

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

scientific article

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

scientific article published on 13 September 2013

Reactions graphs

article

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

scientific article published on 28 April 2010

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

scientific article

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

scientific article published on 10 May 2008

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

scientific article published in August 1997

Ribosomal RNA Kink-turn Motif—A Flexible Molecular Hinge

scientific article published in October 2004

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

scientific article

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

scientific article published on 19 June 2020

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

scientific article

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.

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 21 May 2013

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

scientific article published on August 2006

Structures and mechanisms of glycosyltransferases

scientific article

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

scientific article published on 10 September 2012

TRITON: a graphical tool for ligand-binding protein engineering

scientific article published on 4 July 2008

TRITON: graphic software for rational engineering of enzymes.

scientific article

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

scientific article published in September 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

scientific article (publication date: 17 October 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

scientific article

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

scientific article published on 27 January 2016

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

scientific article published on 8 April 2011

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

scientific article published in October 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

scientific article

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

scientific article

Visualization and Analysis of Protein Structures with LiteMol Suite

scientific article published on 01 January 2020

Why acetylcholinesterase reactivators do not work in butyrylcholinesterase

scientific article published on June 2010

List of works by Jaroslav Koča

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

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

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

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

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

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

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

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

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

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

Anatomy of enzyme channels

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

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

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

Automated Family-Wide Annotation of Secondary Structure Elements

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

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

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

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

Biomacromolecular Fragments and Patterns

Channel Characteristics

ChannelsDB: database of biomacromolecular tunnels and pores

Characterization via Charges

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

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

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.

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

Concluding Remarks

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

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

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

Conformational behavior of insect pheromones and analogues. Part II

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

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

Consistency of sugar structures and their annotation in the PDB.

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

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

Detection and Extraction of Fragments

Detection of Channels

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

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

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

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

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

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

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

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

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

Empirical charges for chemoinformatics applications.

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

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

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation

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

Exercises Solution

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

Extended molecular dynamics of a c-kit promoter quadruplex

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

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

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

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

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

High-performance macromolecular data delivery and visualization for the web

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

High-quality and universal empirical atomic charges for chemoinformatics applications

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

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

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.

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