Jirí Vondrásek

发表

3DPatch: fast 3D structure visualization with residue conservation

Robert D. Finn, David Jakubec, Jirí Vondrásek, 2018, Bioinform..

MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

Nikolay V. Dokholyan, Jirí Vondrásek, Shuangye Yin, 2008, J. Chem. Inf. Model..

Sachem: a chemical cartridge for high-performance substructure search

Miroslav Kratochvíl, Jakub Galgonek, Jirí Vondrásek, 2018, Journal of Cheminformatics.

HIV protease structural database

T. N. Bhat, Gary Gilliland, Veerasamy Ravichandran, 2002, Proceedings. IEEE Computer Society Bioinformatics Conference.

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

Petr Mejzlík, Pavel Hobza, Jirí Vondrásek, 1997, J. Comput. Chem..

Sequence Versus Composition: What Prescribes IDP Biophysical Properties?

Jirí Vondrásek, Klára Hlouchová, Jirí Vymetal, 2019, Entropy.

On InChI and evaluating the quality of cross-reference links

Jakub Galgonek, Jirí Vondrásek, J. Vondrášek, 2014, Journal of Cheminformatics.

Advanced SPARQL querying in small molecule databases

Jakub Galgonek, Vendula Michlíková, Petr Onderka, 2016, Journal of Cheminformatics.

Amino Acid Interaction (INTAA) web server

David Jakubec, Jakub Galgonek, Jirí Vondrásek, 2017, Nucleic Acids Res..

Scalable semi-supervised dimensionality reduction with GPU-accelerated EmbedSOM pdf

Martin Krulis, Miroslav Kratochvíl, Jirí Vondrásek, 2022, ArXiv.

Unexpectedly strong energy stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues: correlated ab initio quantum chemical calculations.

Pavel Hobza, Jirí Vondrásek, Vojtech Klusák, 2005, Journal of the American Chemical Society.

Unusual binding mode of an HIV-1 protease inhibitor explains its potency against multi-drug-resistant virus strains.

Thomas Klimkait, Martin Svec, Jirí Vondrásek, 2002, Journal of molecular biology.

The molecular origin of like-charge arginine-arginine pairing in water.

Jirí Vondrásek, Pavel Jungwirth, J. Heyda, 2009, The journal of physical chemistry. B.

Homology modeling and SAR analysis of Schistosoma japonicum cathepsin D (SjCD) with statin inhibitors identify a unique active site steric barrier with potential for the design of specific inhibitors

Pavel Majer, Jirí Vondrásek, J. Konvalinka, 2005, Biological chemistry.

Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor.

Jirí Cerný, Agnieszka Bronowska, Jirí Vondrásek, 2006, Journal of molecular biology.

Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case study.

Jirí Vondrásek, J. Vymětal, J. Vondrášek, 2010, The journal of physical chemistry. B.