Jirí Vondrásek

20 papers Journal 18Unranked 2
YearRankTypeTitle / Venue / Authors
2024 — conf
CHIST-ERA Triple: improving data interoperability and federation across RDF knowledge graphs and Solid Pods.
SWAT4HCLS
Jerven T. Bolleman, Elias Crum, Iulian Dragan, Jakub Galgonek, Mark Ibberson, Tarcisio Mendes de Farias, Marek Moos, Marco Pagni, Ruben Taelman, Jirí Vondrásek, Ana Claudia Sima
2024 J jnl
The IDSM mass spectrometry extension: searching mass spectra using SPARQL.
Bioinform.
Jakub Galgonek, Jirí Vondrásek
2023 J jnl
A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL.
J. Cheminformatics
Jakub Galgonek, Jirí Vondrásek
2023 J jnl
PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction.
BMC Bioinform.
Katerina Faltejsková, Jirí Vondrásek
2022 J jnl
Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules.
J. Chem. Inf. Model.
Jirí Vymetal, Jirí Vondrásek
2022 J jnl
Scalable semi-supervised dimensionality reduction with GPU-accelerated EmbedSOM.
CoRR
Adam Smelko, Sona Molnárová, Miroslav Kratochvíl, Abhishek Koladiya, Jan Musil, Martin Krulis, Jirí Vondrásek
2021 J jnl
Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures.
Nucleic Acids Res.
Jirí Vymetal, David Jakubec, Jakub Galgonek, Jirí Vondrásek
2021 J jnl
IDSM ChemWebRDF: SPARQLing small-molecule datasets.
J. Cheminformatics
Jakub Galgonek, Jirí Vondrásek
2020 J jnl
Correction to: Interoperable chemical structure search service.
J. Cheminformatics
Miroslav Kratochvíl, Jirí Vondrásek, Jakub Galgonek
2020 J jnl
ShinySOM: graphical SOM-based analysis of single-cell cytometry data.
Bioinform.
Miroslav Kratochvíl, David Bednárek, Tomás Sieger, Karel Fiser, Jirí Vondrásek
2019 J jnl
3DPatch: fast 3D structure visualization with residue conservation.
Bioinform.
David Jakubec, Jirí Vondrásek, Robert D. Finn
2019 J jnl
Interoperable chemical structure search service.
J. Cheminformatics
Miroslav Kratochvíl, Jirí Vondrásek, Jakub Galgonek
2019 J jnl
Sequence Versus Composition: What Prescribes IDP Biophysical Properties?
Entropy
Jirí Vymetal, Jirí Vondrásek, Klára Hlouchová
2018 J jnl
Sachem: a chemical cartridge for high-performance substructure search.
J. Cheminformatics
Miroslav Kratochvíl, Jirí Vondrásek, Jakub Galgonek
2017 J jnl
Amino Acid Interaction (INTAA) web server.
Nucleic Acids Res.
Jakub Galgonek, Jirí Vymetal, David Jakubec, Jirí Vondrásek
2016 J jnl
Advanced SPARQL querying in small molecule databases.
J. Cheminformatics
Jakub Galgonek, Tomás Hurt, Vendula Michlíková, Petr Onderka, Jan Schwarz, Jirí Vondrásek
2014 J jnl
On InChI and evaluating the quality of cross-reference links.
J. Cheminformatics
Jakub Galgonek, Jirí Vondrásek
2008 J jnl
MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening.
J. Chem. Inf. Model.
Shuangye Yin, Lada Biedermannová, Jirí Vondrásek, Nikolay V. Dokholyan
2002 — conf
HIV Protease Structural Database.
CSB
Veerasamy Ravichandran, Jirí Vondrásek, Gary Gilliland, T. N. Bhat, Alexander Wlodawer
1997 J jnl
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.
Pavel Hobza, Martin Kabelác, Jirí Sponer, Petr Mejzlík, Jirí Vondrásek