Jirí Vondrásek

Publication Activity (10 Years)

Years Active: 1997-2023
Publications (10 Years): 14

Top Topics

Search Computing

Protein Function

Dimensionality Reduction

Top Venues

J. Cheminformatics

Nucleic Acids Res.

Publications

Jakub Galgonek, Jirí Vondrásek
A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL. J. Cheminformatics 15 (1) (2023)
Katerina Faltejsková, Jirí Vondrásek
PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction. BMC Bioinform. 24 (1) (2023)
Jirí Vymetal, Jirí Vondrásek
Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules. J. Chem. Inf. Model. 62 (19) (2022)
Adam Smelko, Sona Molnárová, Miroslav Kratochvíl, Abhishek Koladiya, Jan Musil, Martin Krulis, Jirí Vondrásek
Scalable semi-supervised dimensionality reduction with GPU-accelerated EmbedSOM. CoRR (2022)
Jirí Vymetal, David Jakubec, Jakub Galgonek, Jirí Vondrásek
Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Jakub Galgonek, Jirí Vondrásek
IDSM ChemWebRDF: SPARQLing small-molecule datasets. J. Cheminformatics 13 (1) (2021)
Miroslav Kratochvíl, Jirí Vondrásek, Jakub Galgonek
Correction to: Interoperable chemical structure search service. J. Cheminformatics 12 (1) (2020)
Miroslav Kratochvíl, David Bednárek, Tomás Sieger, Karel Fiser, Jirí Vondrásek
ShinySOM: graphical SOM-based analysis of single-cell cytometry data. Bioinform. 36 (10) (2020)
David Jakubec, Jirí Vondrásek, Robert D. Finn
3DPatch: fast 3D structure visualization with residue conservation. Bioinform. 35 (2) (2019)
Jirí Vymetal, Jirí Vondrásek, Klára Hlouchová
Sequence Versus Composition: What Prescribes IDP Biophysical Properties? Entropy 21 (7) (2019)
Miroslav Kratochvíl, Jirí Vondrásek, Jakub Galgonek
Interoperable chemical structure search service. J. Cheminformatics 11 (1) (2019)
Miroslav Kratochvíl, Jirí Vondrásek, Jakub Galgonek
Sachem: a chemical cartridge for high-performance substructure search. J. Cheminformatics 10 (1) (2018)
Jakub Galgonek, Jirí Vymetal, David Jakubec, Jirí Vondrásek
Amino Acid Interaction (INTAA) web server. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Jakub Galgonek, Tomás Hurt, Vendula Michlíková, Petr Onderka, Jan Schwarz, Jirí Vondrásek
Advanced SPARQL querying in small molecule databases. J. Cheminformatics 8 (1) (2016)
Jakub Galgonek, Jirí Vondrásek
On InChI and evaluating the quality of cross-reference links. J. Cheminformatics 6 (1) (2014)
Shuangye Yin, Lada Biedermannová, Jirí Vondrásek, Nikolay V. Dokholyan
MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening. J. Chem. Inf. Model. 48 (8) (2008)
Veerasamy Ravichandran, Jirí Vondrásek, Gary Gilliland, T. N. Bhat, Alexander Wlodawer
HIV Protease Structural Database. CSB (2002)
Pavel Hobza, Martin Kabelác, Jirí Sponer, Petr Mejzlík, Jirí Vondrásek
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. J. Comput. Chem. 18 (9) (1997)