Jiří Vondrášek

发表

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

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

Generalized EmbedSOM on quadtree-structured self-organizing maps

Jiří Vondrášek, Miroslav Kratochvíl, Abhishek Koladiya, 2019, F1000Research.

Rapid single-cell cytometry data visualization with EmbedSOM

Karel Drbal, Miroslav Kratochvíl, Jiří Vondrášek, 2018 .

GigaSOM.jl: Huge-scale, high-performance flow cytometry clustering with Julia

Christophe Trefois, Miroslav Kratochvíl, Jiří Vondrášek, 2020 .

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

Reinhard Schneider, Christophe Trefois, Jiří Vondrášek, 2020, GigaScience.

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

Jiří Vondrášek, Miroslav Kratochvíl, Radislav Sedlacek, 2019 .

Correction to: Interoperable chemical structure search service

Jiří Vondrášek, Jakub Galgonek, Miroslav Kratochvíl, 2020, J. Cheminformatics.

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

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

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

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

Interoperable chemical structure search service

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

IDSM ChemWebRDF: SPARQLing small-molecule datasets

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

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

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

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

Jiří Vondrášek, Martin Hubálek, Lucie Bednárová, 2017, Scientific Reports.

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

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

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

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

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

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

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 .

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 .

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

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

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.

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.

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

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