J. Vondrášek

发表

Insights into Unfolded Proteins from the Intrinsic ϕ/ψ Propensities of the AAXAA Host-Guest Series.

Valerie Daggett, Jiri Vondrasek, V. Daggett, 2016, Biophysical journal.

Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition.

J. Vymětal, J. Vondrášek, J. Černý, 2014, Protein engineering, design & selection : PEDS.

Optimal definition of inter-residual contact in globular proteins based on pairwise interaction energy calculations, its robustness, and applications.

J. Vondrášek, B. Fačkovec, 2012, The journal of physical chemistry. B.

Novel high‐affinity binders of human interferon gamma derived from albumin‐binding domain of protein G

Jiří Vondrášek, Petr Malý, Lada Biedermannová, 2012, Proteins.

Inhibitors of HIV-1 protease: a major success of structure-assisted drug design.

A Wlodawer, A. Wlodawer, J. Vondrášek, 1998, Annual review of biophysics and biomolecular structure.

Structure and IR spectrum of phenylalanyl-glycyl-glycine tripetide in the gas-phase: IR/UV experiments, ab initio quantum chemical calculations, and molecular dynamic simulations.

J. Vondrášek, P. Hobza, M. de Vries, 2005, Chemistry.

Critical Assessment of Current Force Fields. Short Peptide Test Case.

J. Vymětal, J. Vondrášek, 2013, Journal of chemical theory and computation.

Enzyme catalysis prior to aromatic residues: reverse engineering of a dephosphoCoA kinase

A. Dunker, J. Meng, J. Vondrášek, 2020, bioRxiv.

The molecular origin of like-charge arginine-arginine pairing in water.

Jirí Vondrásek, Pavel Jungwirth, J. Heyda, 2009, The journal of physical chemistry. B.

Like-charge guanidinium pairing from molecular dynamics and ab initio calculations.

Mario Vazdar, Pavel Jungwirth, J. Heyda, 2011, The journal of physical chemistry. A.

HIVdb: A Database of the Structures of Human Immunodeficiency Virus Protease

Alexander Wlodawer, Jiri Vondrasek, A. Wlodawer, 2002, Proteins.

Towards a better understanding of the specificity of protein–protein interaction

J. Vondrášek, J. Kysilka, 2012, Journal of molecular recognition : JMR.

TRPM 6 N-Terminal CaM-and S 100 A 1-Binding Domains

J. Vondrášek, P. Heřman, M. Zouharova, 2019 .

TRPM6 N-Terminal CaM- and S100A1-Binding Domains

J. Vondrášek, P. Heřman, K. Hofbauerová, 2019, International journal of molecular sciences.

Representative Amino Acid Side-Chain Interactions in Protein-DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems.

R. Laskowski, J. Vondrášek, Ramachandran Gnanasekaran, 2015, Journal of chemical theory and computation.

Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation

J. Vondrášek, David Jakubec, Kateřina Faltejsková, 2020, International journal of molecular sciences.

Decomposition of Intramolecular Interactions Between Amino-Acids in Globular Proteins - A Consequence for Structural Classes of Proteins and Methods of Their Classification

J. Vondrášek, B. Fačkovec, 2011 .

Artificial proteins as allosteric modulators of PDZ3 and SH3 in two‐domain constructs: A computational characterization of novel chimeric proteins

J. Vondrášek, V. Obsilova, L. Bednárová, 2016, Proteins.

Shared CaM‐ and S100A1‐binding epitopes in the distal TRPM4 N terminus

L. Vyklický, J. Vondrášek, P. Heřman, 2018, The FEBS journal.

The characterization of a novel S100A1 binding site in the N-terminus of TRPM1.

L. Vyklický, J. Vondrášek, M. Sulc, 2016, The international journal of biochemistry & cell biology.

A systematic method for analysing the protein hydration structure of T4 lysozyme

J. Vondrášek, J. Kysilka, 2013, Journal of molecular recognition : JMR.

The DF-LCCSD(T0) correction of the φ/ψ force field dihedral parameters significantly influences the free energy profile of the alanine dipeptide

J. Vymětal, J. Vondrášek, 2011 .

Mapping the pro-peptide of the Schistosoma mansoni cathepsin B1 drug target: modulation of inhibition by heparin and design of mimetic inhibitors.

J. Vondrášek, C. Caffrey, Conor R Caffrey, 2011, ACS chemical biology.

Novel Structural Mechanism of Allosteric Regulation of Aspartic Peptidases via an Evolutionarily Conserved Exosite.

O. Schueler‐Furman, J. Vondrášek, J. Brynda, 2018, Cell chemical biology.

SmSP2: A serine protease secreted by the blood fluke pathogen Schistosoma mansoni with anti-hemostatic properties

C. Craik, J. Dvorak, J. Vondrášek, 2018, PLoS neglected tropical diseases.

Prolyl Oligopeptidase from the Blood Fluke Schistosoma mansoni: From Functional Analysis to Anti-schistosomal Inhibitors

J. Dvorak, J. Vondrášek, J. McKerrow, 2015, PLoS neglected tropical diseases.

Activation route of the Schistosoma mansoni cathepsin B1 drug target: structural map with a glycosaminoglycan switch.

J. Vondrášek, J. McKerrow, J. Brynda, 2014, Structure.

Cathepsin D propeptide: mechanism and regulation of its interaction with the catalytic core.

J. Ježek, J. Vondrášek, L. Marešová, 2006, Biochemistry.

The identification of new substrates of human DHRS7 by molecular modeling and in vitro testing.

J. Vondrášek, P. Kirubakaran, H. Štambergová, 2017, International journal of biological macromolecules.

An intrinsically disordered proteins community for ELIXIR

Silvio C. E. Tosatto, Richard J. Edwards, Norman E. Davey, 2019, F1000Research.

Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes.

R. Laskowski, J. Vondrášek, P. Hobza, 2015, Journal of Chemical Theory and Computation.

An intrinsically disordered proteins community for ELIXIR [version 1; peer review: 2 approved]

Richard J. Edwards, Philippe Le Mercier, J. M. Hancock, 2020 .

The LOTUS initiative for open knowledge management in natural products research

C. Steinbeck, R. Page, D. Mietchen, 2022, eLife.

Bioinformatic analysis and molecular modelling of human ameloblastin suggest a two-domain intrinsically unstructured calcium-binding protein.

J. Vymětal, J. Vondrášek, I. Slabý, 2008, European journal of oral sciences.

How to fragment a polypeptide? An ab initio computational study of pair interactions between amino acids and ligand-amino acids in proteins

J. Vondrášek, J. Černý, P. Dobes, 2011 .

Solid phase synthesis of glycopeptide dendrimers with Tn antigenic structure and their biological activities. Part I

J. Ježek, J. Vondrášek, M. Ledvina, 1999 .

An ameloblastin C-terminus variant is present in human adipose tissue

J. Reseland, J. Vondrášek, S. Lyngstadaas, 2018, Heliyon.

Characterization of the part of N-terminal PIP2 binding site of the TRPM1 channel.

L. Vyklický, J. Vondrášek, L. Bumba, 2015, Biophysical chemistry.

Model of peptide bond-aromatic ring interaction: correlated ab initio quantum chemical study.

J. Vondrášek, P. Hobza, P. Jurečka, 2007, The journal of physical chemistry. B.

Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules

J. Vymětal, J. Vondrášek, 2022, J. Chem. Inf. Model..

Intrinsically Disordered Enamel Matrix Protein Ameloblastin Forms Ribbon-like Supramolecular Structures via an N-Terminal Segment Encoded by Exon 5* S

O. Benada, L. Rezabkova, J. Vondrášek, 2013 .

Intrinsically disordered protein domain of human ameloblastin in synthetic fusion with calmodulin increases calmodulin stability and modulates its function.

J. Vymětal, J. Vondrášek, P. Heřman, 2020, International journal of biological macromolecules.

Parametrization of 2,2,2-trifluoroethanol based on the generalized AMBER force field provides realistic agreement between experimental and calculated properties of pure liquid as well as water-mixed solutions.

J. Vymětal, J. Vondrášek, 2014, The journal of physical chemistry. B.

Ameloblastin Peptides Modulates the Osteogenic Capacity of Human Mesenchymal Stem Cells

J. Reseland, J. Vondrášek, S. Lyngstadaas, 2017, Front. Physiol..

Rigid duplex alpha-cyclodextrin reversibly connected with disulfide bonds. Synthesis and inclusion complexes.

J. Vymětal, J. Vondrášek, J. Černý, 2009, The Journal of organic chemistry.

Fusion of two unrelated protein domains in a chimera protein and its 3D prediction: Justification of the x‐ray reference structures as a prediction benchmark

K. Mertová, J. Vymětal, J. Vondrášek, 2022, Proteins.

Loss of dispersion energy changes the stability and folding/unfolding equilibrium of the Trp-cage protein.

J. Vondrášek, J. Černý, P. Hobza, 2009, The journal of physical chemistry. B.

Structure and Stability of the Water−Graphite Complexes

J. Vondrášek, P. Nachtigall, O. Bludský, 2009 .

Substituents at the C3′ and C3′N positions are critical for taxanes to overcome acquired resistance of cancer cells to paclitaxel

J. Vondrášek, J. Kovář, Vlasta Němcová-Fürstová, 2018, Toxicology and applied pharmacology.

SERINE PHOSPHORYLATION EFFECT ON SECONDARY STRUCTURE PREDICTION OF INTRINSICALLY UNSTRUCTURED AND ORDERED STRUCTURED PENTAPEPTIDES BY RAMACHANDRAN ANALYSIS

Simon M. Longela, J. Vymětal, J. Vondrášek, 2016 .

Characterization of AMBN I and II Isoforms and Study of Their Ca2+-Binding Properties

J. Reseland, J. Vymětal, J. Vondrášek, 2020, International journal of molecular sciences.

Intrinsically Disordered Enamel Matrix Protein Ameloblastin Forms Ribbon-like Supramolecular Structures via an N-terminal Segment Encoded by Exon 5*

O. Benada, L. Rezabkova, J. Vondrášek, 2013, The Journal of Biological Chemistry.

Phosphorylation Modulates Ameloblastin Self-assembly and Ca2+ Binding

J. Reseland, J. Vondrášek, B. Thiede, 2017, Front. Physiol..

Biophysical characterization of recombinant human ameloblastin.

J. Vondrášek, R. Osicka, M. Sulc, 2011, European journal of oral sciences.

Homology modeling and SAR analysis of Schistosoma japonicum cathepsin D (SjCD) with statin inhibitors identify a unique active site steric barrier with potential for the design of specific inhibitors

Pavel Majer, Jirí Vondrásek, J. Konvalinka, 2005, Biological chemistry.

Quasiplanarity of the peptide bond.

J. Vondrášek, J. Chalupský, V. Špirko, 2008, The journal of physical chemistry. A.

Quantification and rationalization of the higher affinity of sodium over potassium to protein surfaces

J. Vondrášek, P. Jungwirth, B. Jagoda-Cwiklik, 2006, Proceedings of the National Academy of Sciences.

Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree–Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree–Fock results

Pavel Hobza, Jiří Vondrášek, Jiří Šponer, 1997 .

Urea and guanidinium induced denaturation of a Trp-cage miniprotein.

Jiří Vondrášek, Pavel Jungwirth, J. Heyda, 2011, The journal of physical chemistry. B.

Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis

David Jakubec, Roman A. Laskowski, Jiri Vondrasek, 2016, PloS one.

Peptide inhibitors of HIV-1 and HIV-2 proteases: a comparative study.

I. Pichová, J. Konvalinka, P. Štrop, 1997, Leukemia.

Configurations of diastereomeric hydroxyethylene isosteres strongly affect biological activities of a series of specific inhibitors of human-immunodeficiency-virus proteinase.

I. Pichová, J. Konvalinka, P. Štrop, 1997, European journal of biochemistry.

Early evolution of enamel matrix proteins is reflected by pleiotropy of physiological functions

J. Reseland, J. Vondrášek, R. Osicka, 2023, Scientific Reports.

Hypertrophic cardiomyopathy: from mutation to functional analysis of defective protein

J. Vondrášek, R. Brdička, P. Čapek, 2011, Croatian medical journal.

Random protein sequences can form defined secondary structures and are well-tolerated in vivo

J. Konvalinka, J. Vymětal, J. Vondrášek, 2017, Scientific Reports.

Potency comparison of peptidomimetic inhibitors against HIV-1 and HIV-2 proteinases: design of equipotent lead compounds.

I. Pichová, J. Urban, J. Konvalinka, 1997, Archives of biochemistry and biophysics.

Database of three-dimensional structures of HIV proteinases

Alexander Wlodawer, Jiri Vondrasek, Christopher P. van Buskirk, 1997, Nature Structural Biology.

A community proposal to integrate proteomics activities in ELIXIR

Lennart Martens, Martin Eisenacher, Wout Bittremieux, 2017, F1000Research.

Highly selective purification of three lipases from Geotrichum candidum 4013 and their characterization and biotechnological applications

J. Vondrášek, Z. Demianová, J. Palomo, 2013 .

TRPM7 N-terminal region forms complexes with calcium binding proteins CaM and S100A1

J. Vondrášek, P. Heřman, M. Zouharova, 2021, Heliyon.

Mapping of CaM, S100A1 and PIP2-Binding Epitopes in the Intracellular N- and C-Termini of TRPM4

J. Vondrášek, I. Barvík, P. Heřman, 2020, International journal of molecular sciences.

Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane.

Karel Berka, Pavel Hobza, Jiri Vondrasek, 2008, Physical chemistry chemical physics : PCCP.

GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets

Christophe Trefois, Reinhard Schneider, Venkata P. Satagopam, 2020, bioRxiv.

Trypsin- and Chymotrypsin-Like Serine Proteases in Schistosoma mansoni – ‘The Undiscovered Country’

Anna V. Protasio, Jiří Vondrášek, Jan Dvořák, 2014, PLoS neglected tropical diseases.

Magnesium and biological activity of oxytocin analogues modified on aromatic ring of amino acid in position 2

J. Vondrášek, J. Slaninová, L. Maletínská, 2001, Journal of peptide science : an official publication of the European Peptide Society.

Increasing Affinity of Interferon-γ Receptor 1 to Interferon-γ by Computer-Aided Design

Jiří Vondrášek, Petr Malý, Jiří Černý, 2013, BioMed research international.

Scalable semi-supervised dimensionality reduction with GPU-accelerated EmbedSOM pdf

Martin Krulis, Miroslav Kratochvíl, Jirí Vondrásek, 2022, ArXiv.

Free‐thiol Cys331 exposed during activation process is critical for native tetramer structure of cathepsin C (dipeptidyl peptidase I)

J. Vondrášek, Z. Voburka, M. Horn, 2002, Protein science : a publication of the Protein Society.

ShinySOM: graphical SOM-based analysis of single-cell cytometry data

David Bednárek, Jiří Vondrášek, Miroslav Kratochvíl, 2020, Bioinform..

Effect of enamel matrix derivative and of proline-rich synthetic peptides on the differentiation of human mesenchymal stem cells toward the osteogenic lineage.

J. Vondrášek, M. Monjo, M. Rubert, 2012, Tissue engineering. Part A.

Generalized EmbedSOM on quadtree-structured self-organizing maps.

J. Vondrášek, Miroslav Kratochvíl, A. Koladiya, 2019, F1000Research.

Exquisite ligand stereoselectivity of a Drosophila juvenile hormone receptor contrasts with its broad agonist repertoire

R. Hanus, J. Vondrášek, P. Jedlička, 2018, The Journal of Biological Chemistry.

MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

Nikolay V. Dokholyan, Jirí Vondrásek, Shuangye Yin, 2008, J. Chem. Inf. Model..

Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures.

Karel Berka, Pavel Hobza, Kevin E. Riley, 2009, Journal of chemical theory and computation.

The Stabilization Energy of the GLU-LYS Salt Bridge in the Protein/Water Environment: Correlated Quantum Chemical ab initio , DFT and Empirical Potential Studies

K. Berka, J. Vondrášek, P. Hobza, 2008 .

Unusual binding mode of an HIV-1 protease inhibitor explains its potency against multi-drug-resistant virus strains.

Thomas Klimkait, Martin Svec, Jirí Vondrásek, 2002, Journal of molecular biology.

TRPM5 Channel Binds Calcium-Binding Proteins Calmodulin and S100A1.

J. Vymětal, J. Vondrášek, P. Heřman, 2022, Biochemistry.

Advanced SPARQL querying in small molecule databases

Jakub Galgonek, Vendula Michlíková, Petr Onderka, 2016, Journal of Cheminformatics.

The LOTUS Initiative for Open Natural Products Research: Knowledge Management through Wikidata

C. Steinbeck, Egon Willighagen, R. Page, 2021, bioRxiv.

Effect of TFE on the Helical Content of AK17 and HAL-1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization.

J. Vymětal, J. Vondrášek, L. Bednárová, 2016, The journal of physical chemistry. B.

Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web

J. Damborský, J. Vondrášek, D. Bednář, 2022, Computational and structural biotechnology journal.

IDSM ChemWebRDF: SPARQLing small-molecule datasets

Jiří Vondrášek, Jakub Galgonek, J. Vondrášek, 2021, Journal of Cheminformatics.

Interoperable chemical structure search service

Miroslav Kratochvíl, Jiří Vondrášek, Jakub Galgonek, 2019, Journal of Cheminformatics.

3DPatch: fast 3D structure visualization with residue conservation

Robert D. Finn, David Jakubec, Jirí Vondrásek, 2018, Bioinform..

Widespread evolutionary crosstalk among protein domains in the context of multi-domain proteins

David Jakubec, Miroslav Kratochvíl, Jiří Vymĕtal, 2018, PloS one.

Performance of the DFT-D method, paired with the PCM implicit solvation model, for the computation of interaction energies of solvated complexes of biological interest.

Kevin E. Riley, J. Vondrášek, P. Hobza, 2007, Physical chemistry chemical physics : PCCP.

The order of PDZ3 and TrpCage in fusion chimeras determines their properties—a biophysical characterization

J. Vondrášek, O. Vaněk, K. Tripsianes, 2021, Protein science : a publication of the Protein Society.

New database.

A Wlodawer, A. Wlodawer, J. Vondrášek, 1996, Science.

Efficient Estimation of Absolute Binding Free Energy for a Homeodomain-DNA Complex from Non-Equilibrium Pulling Simulations.

J. Vondrášek, David Jakubec, 2020, Journal of chemical theory and computation.

Can All-Atom Molecular Dynamics Simulations Quantitatively Describe Homeodomain-DNA Binding Equilibria?

J. Vondrášek, David Jakubec, 2019, Journal of chemical theory and computation.

Sexual attraction in the silkworm moth. Nature of binding of bombykol in pheromone binding protein--an ab initio study.

J. Vondrášek, A. Svatoš, L. Rulíšek, 2003, Chemistry & biology.

AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation.

J. Vymětal, J. Vondrášek, V. Jurásková, 2018, Journal of chemical theory and computation.

The bio.tools registry of software tools and data resources for the life sciences

Arlindo L. Oliveira, Rob W.W. Hooft, S. Brunak, 2019, Genome Biology.

Gyration- and inertia-tensor-based collective coordinates for metadynamics. Application on the conformational behavior of polyalanine peptides and Trp-cage folding.

Jiří Vondrášek, J. Vymětal, J. Vondrášek, 2011, The journal of physical chemistry. A.

Sachem: a chemical cartridge for high-performance substructure search

Miroslav Kratochvíl, Jakub Galgonek, Jirí Vondrásek, 2018, Journal of Cheminformatics.

Open Natural Products Research: Curation and Dissemination of Biological Occurrences of Chemical Structures through Wikidata

C. Steinbeck, Egon Willighagen, R. Page, 2021 .

Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples

Karel Berka, Pavel Hobza, Kevin E. Riley, 2008 .

Unexpectedly strong energy stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues: correlated ab initio quantum chemical calculations.

Pavel Hobza, Jirí Vondrásek, Vojtech Klusák, 2005, Journal of the American Chemical Society.

Sequence Versus Composition: What Prescribes IDP Biophysical Properties?

Jirí Vondrásek, Klára Hlouchová, Jirí Vymetal, 2019, Entropy.

Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho‐CoA kinase

A. Dunker, J. Vondrášek, P. Srb, 2021, Protein science : a publication of the Protein Society.

Structured proteins are abundant in unevolved sequence space

J. Vymětal, J. Vondrášek, K. Fujishima, 2021, bioRxiv.

Analysis of energy stabilization inside the hydrophobic core of rubredoxin.

K. Berka, J. Vondrášek, P. Hobza, 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.

A picomolar inhibitor of resistant strains of human immunodeficiency virus protease identified by a combinatorial approach.

T. Klimkait, J. Konvalinka, J. Vondrášek, 2000, Archives of biochemistry and biophysics.

Ion specific effects of sodium and potassium on the catalytic activity of HIV-1 protease.

J. Heyda, J. Konvalinka, J. Vondrášek, 2009, Physical chemistry chemical physics : PCCP.

Dispersion interactions govern the strong thermal stability of a protein.

J. Vondrášek, J. Černý, V. Sklenar, 2007, Chemistry.

Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures

J. Vymětal, J. Vondrášek, David Jakubec, 2021, Nucleic Acids Res..

Computational methods for the description of pharmacologically relevant platinum complexes--molecular structure and bond dissociation.

J. Vondrášek, P. Hobza, Jakub Galgonek, 2016, Physical chemistry chemical physics : PCCP.

On InChI and evaluating the quality of cross-reference links

Jakub Galgonek, Jirí Vondrásek, J. Vondrášek, 2014, Journal of Cheminformatics.

Chemical compound navigator: A web‐based chem‐BLAST, chemical taxonomy‐based search engine for browsing compounds

Alexander Wlodawer, M D Prasanna, Jiri Vondrasek, 2006, Proteins.

Application of InChI to curate, index, and query 3‐D structures

Alexander Wlodawer, M D Prasanna, Jiri Vondrasek, 2005, Proteins.

SOM-based embedding improves efficiency of high-dimensional cytometry data analysis

Jiří Vondrášek, Miroslav Kratochvíl, Radislav Sedlacek, 2019 .

Rapid single-cell cytometry data visualization with EmbedSOM

Karel Drbal, Miroslav Kratochvíl, Jiří Vondrášek, 2018 .

Modern and prebiotic amino acids support distinct structural profiles in proteins

J. Vymětal, J. Vondrášek, K. Fujishima, 2022, Open Biology.

The bio.tools registry of software tools and data resources for the life sciences

Hedi Peterson, Tomáš Raček, Radka Svobodová Vařeková, 2019, Genome Biology.

Synthetic Peptides Analogue to Enamel Proteins Promote Osteogenic Differentiation of MC3T3-E1 and Mesenchymal Stem Cells

J. Vondrášek, M. Monjo, M. Rubert, 2011 .

Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case study.

Jirí Vondrásek, J. Vymětal, J. Vondrášek, 2010, The journal of physical chemistry. B.

PIP2 and PIP3 interact with N-terminus region of TRPM4 channel.

L. Vyklický, J. Vondrášek, L. Bumba, 2015, Biophysical chemistry.

Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins.

R. Laskowski, K. Berka, J. Vondrášek, 2010, Journal of chemical theory and computation.

Identifying stabilizing key residues in proteins using interresidue interaction energy matrix

J. Vondrášek, P. Hobza, Lada Bendová-Biedermannová, 2008, Proteins.

Amino Acid Interaction (INTAA) web server

David Jakubec, Jakub Galgonek, Jirí Vondrásek, 2017, Nucleic Acids Res..

Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes.

Pavel Hobza, David Jakubec, Jiří Vondrášek, 2017, Journal of chemical theory and computation.

Ability of empirical potentials (AMBER, CHARMM, CVFF, OPLS, Poltev) and semi-empirical quantum chemical methods (AM1, MNDO/M, PM3) to describe H-bonding in DNA base pairs; comparison with ab initio results

J. Šponer, J. Vondrášek, P. Hobza, 1996 .

A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL

J. Vondrášek, Jakub Galgonek, 2023, Journal of Cheminformatics.

Regioselective Palmitoylation of 9-(2,3-Dihydroxy- propyl)adenine Catalyzed by a Glycopolymer-enzyme Conjugate

J. Vondrášek, J. Palomo, M. Krečmerová, 2016, Molecules.

Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor.

Jirí Cerný, Agnieszka Bronowska, Jirí Vondrásek, 2006, Journal of molecular biology.