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; Martin Kabelác; Jirí Sponer; Petr Mejzlík; Jirí Vondrásek (J. Comput. Chem., 1997)

HIV Protease Structural Database. - Veerasamy Ravichandran; Jirí Vondrásek; Gary Gilliland; T. N. Bhat; Alexander Wlodawer (CSB, 2002)

MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening. - Shuangye Yin; Lada Biedermannová; Jirí Vondrásek; Nikolay V. Dokholyan (J. Chem. Inf. Model., 2008)

On InChI and evaluating the quality of cross-reference links. - Jakub Galgonek; Jirí Vondrásek (J. Cheminformatics, 2014)

Advanced SPARQL querying in small molecule databases. - Jakub Galgonek; Tomás Hurt; Vendula Michlíková; Petr Onderka; Jan Schwarz; Jirí Vondrásek (J. Cheminformatics, 2016)

Amino Acid Interaction (INTAA) web server. - Jakub Galgonek; Jirí Vymetal; David Jakubec; Jirí Vondrásek (Nucleic Acids Res., 2017)

Sachem: a chemical cartridge for high-performance substructure search. - Miroslav Kratochvíl; Jirí Vondrásek; Jakub Galgonek (J. Cheminformatics, 2018)

3DPatch: fast 3D structure visualization with residue conservation. - David Jakubec; Jirí Vondrásek; Robert D. Finn (Bioinform., 2019)

Sequence Versus Composition: What Prescribes IDP Biophysical Properties? - Jirí Vymetal; Jirí Vondrásek; Klára Hlouchová (Entropy, 2019)

Interoperable chemical structure search service. - Miroslav Kratochvíl; Jirí Vondrásek; Jakub Galgonek (J. Cheminformatics, 2019)

ShinySOM: graphical SOM-based analysis of single-cell cytometry data. - Miroslav Kratochvíl; David Bednárek; Tomás Sieger; Karel Fiser; Jirí Vondrásek (Bioinform., 2020)

Correction to: Interoperable chemical structure search service. - Miroslav Kratochvíl; Jirí Vondrásek; Jakub Galgonek (J. Cheminformatics, 2020)

IDSM ChemWebRDF: SPARQLing small-molecule datasets. - Jakub Galgonek; Jirí Vondrásek (J. Cheminformatics, 2021)

Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures. - Jirí Vymetal; David Jakubec; Jakub Galgonek; Jirí Vondrásek (Nucleic Acids Res., 2021)

Scalable semi-supervised dimensionality reduction with GPU-accelerated EmbedSOM. - Adam Smelko; Sona Molnárová; Miroslav Kratochvíl; Abhishek Koladiya; Jan Musil; Martin Krulis; Jirí Vondrásek (CoRR, 2022)

Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules. - Jirí Vymetal; Jirí Vondrásek (J. Chem. Inf. Model., 2022)

PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction. - Katerina Faltejsková; Jirí Vondrásek (BMC Bioinform., 2023)

A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL. - Jakub Galgonek; Jirí Vondrásek (J. Cheminformatics, 2023)

CHIST-ERA Triple: improving data interoperability and federation across RDF knowledge graphs and Solid Pods. - 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 (SWAT4HCLS, 2024)