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ORCIDJirí Vondrásek
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Journal Articles
- 2023
[j16]Katerina Faltejsková
, Jirí Vondrásek:
PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction. BMC Bioinform. 24(1): 487 (2023)- [j15]Jakub Galgonek, Jirí Vondrásek:
A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL. J. Cheminformatics 15(1): 61 (2023) - 2022
- [j14]Jirí Vymetal, Jirí Vondrásek:
Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules. J. Chem. Inf. Model. 62(19): 4783-4798 (2022) - 2021
- [j13]Jakub Galgonek, Jirí Vondrásek:
IDSM ChemWebRDF: SPARQLing small-molecule datasets. J. Cheminformatics 13(1): 38 (2021) - [j12]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): 15-20 (2021) - 2020
- [j11]Miroslav Kratochvíl, David Bednárek, Tomás Sieger, Karel Fiser, Jirí Vondrásek:
ShinySOM: graphical SOM-based analysis of single-cell cytometry data. Bioinform. 36(10): 3288-3289 (2020) - [j10]Miroslav Kratochvíl, Jirí Vondrásek, Jakub Galgonek:
Correction to: Interoperable chemical structure search service. J. Cheminformatics 12(1): 13 (2020) - 2019
- [j9]David Jakubec, Jirí Vondrásek, Robert D. Finn:
3DPatch: fast 3D structure visualization with residue conservation. Bioinform. 35(2): 332-334 (2019) - [j8]Jirí Vymetal, Jirí Vondrásek, Klára Hlouchová:
Sequence Versus Composition: What Prescribes IDP Biophysical Properties? Entropy 21(7): 654 (2019) - [j7]Miroslav Kratochvíl, Jirí Vondrásek, Jakub Galgonek:
Interoperable chemical structure search service. J. Cheminformatics 11(1): 45:1-45:7 (2019) - 2018
- [j6]Miroslav Kratochvíl, Jirí Vondrásek, Jakub Galgonek:
Sachem: a chemical cartridge for high-performance substructure search. J. Cheminformatics 10(1): 27:1-27:11 (2018) - 2017
- [j5]Jakub Galgonek, Jirí Vymetal, David Jakubec, Jirí Vondrásek:
Amino Acid Interaction (INTAA) web server. Nucleic Acids Res. 45(Webserver-Issue): W388-W392 (2017) - 2016
- [j4]Jakub Galgonek, Tomás Hurt, Vendula Michlíková, Petr Onderka, Jan Schwarz, Jirí Vondrásek:
Advanced SPARQL querying in small molecule databases. J. Cheminformatics 8(1): 31:1-31:14 (2016) - 2014
- [j3]Jakub Galgonek, Jirí Vondrásek:
On InChI and evaluating the quality of cross-reference links. J. Cheminformatics 6(1): 15 (2014) - 2008
- [j2]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): 1656-1662 (2008) - 1997
- [j1]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): 1136-1150 (1997)
Conference and Workshop Papers
- 2002
- [c1]Veerasamy Ravichandran, Jirí Vondrásek, Gary Gilliland, T. N. Bhat, Alexander Wlodawer:
HIV Protease Structural Database. CSB 2002: 340
Informal and Other Publications
- 2022
- [i1]Adam Smelko, Sona Molnárová, Miroslav Kratochvíl, Abhishek Koladiya, Jan Musil, Martin Krulis, Jirí Vondrásek:
Scalable semi-supervised dimensionality reduction with GPU-accelerated EmbedSOM. CoRR abs/2201.00701 (2022)
Coauthor Index
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