Works matching AU Vondrášek, Jiří

Results: 42

GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets.

Published in:

GigaScience, 2020, v. 9, n. 11, p. 1, doi. 10.1093/gigascience/giaa127

By:

Kratochvíl, Miroslav;
Hunewald, Oliver;
Heirendt, Laurent;
Verissimo, Vasco;
Vondrášek, Jiří;
Satagopam, Venkata P;
Schneider, Reinhard;
Trefois, Christophe;
Ollert, Markus

Publication type:

Article

Towards a better understanding of the specificity of protein-protein interaction Towards a better understanding of the specificity of protein-protein interaction.

Published in:

Journal of Molecular Recognition, 2012, v. 25, n. 11, p. 604, doi. 10.1002/jmr.2219

By:

Kysilka, Jiří;
Vondrášek, Jiří

Publication type:

Article

The bio.tools registry of software tools and data resources for the life sciences.

Published in:

2019

By:

Ison, Jon;
Ienasescu, Hans;
Chmura, Piotr;
Rydza, Emil;
Ménager, Hervé;
Kalaš, Matúš;
Schwämmle, Veit;
Grüning, Björn;
Beard, Niall;
Lopez, Rodrigo;
Duvaud, Severine;
Stockinger, Heinz;
Persson, Bengt;
Vařeková, Radka Svobodová;
Raček, Tomáš;
Vondrášek, Jiří;
Peterson, Hedi;
Salumets, Ahto;
Jonassen, Inge;
Hooft, Rob

Publication type:

Letter

Advanced SPARQL querying in small molecule databases.

Published in:

Journal of Cheminformatics, 2016, v. 8, n. 1, p. 1, doi. 10.1186/s13321-016-0144-4

By:

Galgonek, Jakub;
Hurt, Tomáš;
Michlíková, Vendula;
Onderka, Petr;
Schwarz, Jan;
Vondrášek, Jiří

Publication type:

Article

On InChI and evaluating the quality of crossreference links.

Published in:

Journal of Cheminformatics, 2014, v. 6, n. 1, p. 1, doi. 10.1186/1758-2946-6-15

By:

Galgonek, Jakub;
Vondrášek, Jiří

Publication type:

Article

On InChI and evaluating the quality of cross-reference links.

Published in:

Journal of Cheminformatics, 2014, v. 6, n. 1, p. 1, doi. 10.1186/1758-2946-6-15

By:

Galgonek, Jakub;
Vondrášek, Jiří

Publication type:

Article

The IDSM mass spectrometry extension: searching mass spectra using SPARQL.

Published in:

Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae174

By:

Galgonek, Jakub;
Vondrášek, Jiří

Publication type:

Article

A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00729-5

By:

Galgonek, Jakub;
Vondrášek, Jiří

Publication type:

Article

Prolyl Oligopeptidase from the Blood Fluke Schistosoma mansoni: From Functional Analysis to Anti-schistosomal Inhibitors.

Published in:

PLoS Neglected Tropical Diseases, 2015, v. 9, n. 6, p. 1, doi. 10.1371/journal.pntd.0003827

By:

Fajtová, Pavla;
Štefanić, Saša;
Hradilek, Martin;
Dvořák, Jan;
Vondrášek, Jiří;
Jílková, Adéla;
Ulrychová, Lenka;
McKerrow, James H.;
Caffrey, Conor R.;
Mareš, Michael;
Horn, Martin

Publication type:

Article

Prolyl Oligopeptidase from the Blood Fluke Schistosoma mansoni: From Functional Analysis to Anti-schistosomal Inhibitors.

Published in:

PLoS Neglected Tropical Diseases, 2015, v. 9, n. 6, p. 1, doi. 10.1371/journal.pntd.0003827

By:

Fajtová, Pavla;
Štefanić, Saša;
Hradilek, Martin;
Dvořák, Jan;
Vondrášek, Jiří;
Jílková, Adéla;
Ulrychová, Lenka;
McKerrow, James H.;
Caffrey, Conor R.;
Mareš, Michael;
Horn, Martin

Publication type:

Article

Trypsin- and Chymotrypsin-Like Serine Proteases in Schistosoma mansoni – 'The Undiscovered Country'.

Published in:

PLoS Neglected Tropical Diseases, 2014, v. 8, n. 3, p. 1, doi. 10.1371/journal.pntd.0002766

By:

Horn, Martin;
Fajtová, Pavla;
Rojo Arreola, Liliana;
Ulrychová, Lenka;
Bartošová-Sojková, Pavla;
Franta, Zdeněk;
Protasio, Anna V.;
Opavský, David;
Vondrášek, Jiří;
McKerrow, James H.;
Mareš, Michael;
Caffrey, Conor R.;
Dvořák, Jan

Publication type:

Article

Trypsin- and Chymotrypsin-Like Serine Proteases in <i>Schistosoma mansoni</i> – ‘The Undiscovered Country’.

Published in:

PLoS Neglected Tropical Diseases, 2014, v. 8, n. 3, p. 1, doi. 10.1371/journal.pntd.0002766

By:

Horn, Martin;
Fajtová, Pavla;
Rojo Arreola, Liliana;
Ulrychová, Lenka;
Bartošová-Sojková, Pavla;
Franta, Zdeněk;
Protasio, Anna V.;
Opavský, David;
Vondrášek, Jiří;
McKerrow, James H.;
Mareš, Michael;
Caffrey, Conor R.;
Dvořák, Jan

Publication type:

Article

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.

Published in:

Biological Chemistry, 2005, v. 386, n. 4, p. 339, doi. 10.1515/BC.2005.041

By:

Caffrey, Conor R.;
Placha, Lenka;
Barinka, Cyril;
Hradilek, Martin;
Dostal, Jiř;í;
Sajid, Mohammed;
McKerrow, James H.;
Majer, Pavel;
Konvalinka, Jan;
Vondrášek, Jiří

Publication type:

Article

Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin.

Published in:

ChemPhysChem, 2009, v. 10, n. 3, p. 543, doi. 10.1002/cphc.200800401

By:

Berka, Karel;
Hobza, Pavel;
Vondrášek, Jiří

Publication type:

Article

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

Published in:

Journal of Computational Chemistry, 1997, v. 18, n. 9, p. 1136, doi. 10.1002/(SICI)1096-987X(19970715)18:9<1136::AID-JCC3>3.0.CO;2-S

By:

Hobza, Pavel;
Kabeláč, Martin;
Šponer, Jiří;
Mejzlík, Petr;
Vondrášek, Jiří

Publication type:

Article

Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation.

Published in:

International Journal of Molecular Sciences, 2020, v. 21, n. 11, p. 3986, doi. 10.3390/ijms21113986

By:

Faltejsková, Kateřina;
Jakubec, David;
Vondrášek, Jiří

Publication type:

Article

Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho‐CoA kinase.

Published in:

Protein Science: A Publication of the Protein Society, 2021, v. 30, n. 5, p. 1022, doi. 10.1002/pro.4068

By:

Makarov, Mikhail;
Meng, Jingwei;
Tretyachenko, Vyacheslav;
Srb, Pavel;
Březinová, Anna;
Giacobelli, Valerio Guido;
Bednárová, Lucie;
Vondrášek, Jiří;
Dunker, A. Keith;
Hlouchová, Klára

Publication type:

Article

Free-thiol Cys331 exposed during activation process is critical for native tetramer structure of cathepsin C (dipeptidyl peptidase I).

Published in:

Protein Science: A Publication of the Protein Society, 2002, v. 11, n. 4, p. 933, doi. 10.1110/ps.2910102

By:

Horn, Martin;
Baudyš, Miroslav;
Voburka, Zdeněk;
Kluh, Ivan;
Vondrášek, Jiří;
Mareš, Michael

Publication type:

Article

ShinySOM: graphical SOM-based analysis of single-cell cytometry data.

Published in:

Bioinformatics, 2020, v. 36, n. 10, p. 3288, doi. 10.1093/bioinformatics/btaa091

By:

Kratochvíl, Miroslav;
Bednárek, David;
Sieger, Tomáš;
Fišer, Karel;
Vondrášek, Jiří

Publication type:

Article

3DPatch: fast 3D structure visualization with residue conservation.

Published in:

Bioinformatics, 2019, v. 35, n. 2, p. 332, doi. 10.1093/bioinformatics/bty464

By:

Jakubec, David;
Vondrášek, Jiří;
Finn, Robert D

Publication type:

Article

Biophysical characterization of recombinant human ameloblastin.

Published in:

European Journal of Oral Sciences, 2011, v. 119, p. 261, doi. 10.1111/j.1600-0722.2011.00913.x

By:

Wald, Tomáš;
Bednárová, Lucie;
Osička, Radim;
Pachl, Petr;
Šulc, Miroslav;
Lyngstadaas, Stale Petter;
Slaby, Ivan;
Vondrášek, Jiří

Publication type:

Article

Bioinformatic analysis and molecular modelling of human ameloblastin suggest a two-domain intrinsically unstructured calcium-binding protein.

Published in:

European Journal of Oral Sciences, 2008, v. 116, n. 2, p. 124, doi. 10.1111/j.1600-0722.2008.00526.x

By:

Vymětal, Jiří;
Slabý, Ivan;
Spahr, Axel;
Vondrášek, Jiří;
Lyngstadaas, S. Petter

Publication type:

Article

Artificial proteins as allosteric modulators of PDZ3 and SH3 in two-domain constructs: A computational characterization of novel chimeric proteins.

Published in:

Proteins, 2016, v. 84, n. 10, p. 1358, doi. 10.1002/prot.25082

By:

Kirubakaran, Palani;
Pfeiferová, Lucie;
Boušová, Kristýna;
Bednarova, Lucie;
Obšilová, Veronika;
Vondrášek, Jiří

Publication type:

Article

Novel high-affinity binders of human interferon gamma derived from albumin-binding domain of protein G.

Published in:

Proteins, 2012, v. 80, n. 3, p. 774, doi. 10.1002/prot.23234

By:

Ahmad, Jawid N.;
Li, Jingjing;
Biedermannová, Lada;
Kuchař, Milan;
Šípová, Hana;
Semerádtová, Alena;
Černý, Jiří;
Petroková, Hana;
Mikulecký, Pavel;
Polínek, Jiří;
Staněk, Ondřej;
Vondrášek, Jiří;
Homola, Jiří;
Malý, Jan;
Osička, Radim;
Šebo, Peter;
Malý, Petr

Publication type:

Article

Identifying stabilizing key residues in proteins using interresidue interaction energy matrix.

Published in:

Proteins, 2008, v. 72, n. 1, p. 402, doi. 10.1002/prot.21938

By:

Bendová-Biedermannová, Lada;
Hobza, Pavel;
Vondrášek, Jiří

Publication type:

Article

Widespread evolutionary crosstalk among protein domains in the context of multi-domain proteins.

Published in:

PLoS ONE, 2018, v. 13, n. 8, p. 1, doi. 10.1371/journal.pone.0203085

By:

Jakubec, David;
Kratochvíl, Miroslav;
Vymĕtal, Jiří;
Vondrášek, Jiří

Publication type:

Article

Sequence Versus Composition: What Prescribes IDP Biophysical Properties?

Published in:

Entropy, 2019, v. 21, n. 7, p. 654, doi. 10.3390/e21070654

By:

Vymětal, Jiří;
Vondrášek, Jiří;
Hlouchová, Klára

Publication type:

Article

Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures.

Published in:

Nucleic Acids Research, 2021, v. 49, n. W1, p. W15, doi. 10.1093/nar/gkab377

By:

Vymětal, Jiří;
Jakubec, David;
Galgonek, Jakub;
Vondrášek, Jiří

Publication type:

Article

Amino Acid Interaction (INTAA) web server.

Published in:

Nucleic Acids Research, 2017, v. 45, n. W1, p. W388, doi. 10.1093/nar/gkx352

By:

Galgonek, Jakub;
Vymětal, Jiří;
Jakubec, David;
Vondrášek, Jiří

Publication type:

Article

Magnesium and biological activity of oxytocin analogues modified on aromatic ring of amino acid in position 2.

Published in:

Journal of Peptide Science, 2001, v. 7, n. 8, p. 413, doi. 10.1002/psc.334

By:

Slaninová, Jiřina;
Maletínská, Lenka;
Vondrášek, Jiří;
Procházka, Zdenko

Publication type:

Article

Solid phase synthesis of glycopeptide dendrimers with Tn antigenic structure and their biological activities. Part I.

Published in:

Journal of Peptide Science, 1999, v. 5, n. 1, p. 46, doi. 10.1002/(SICI)1099-1387(199901)5:1<46::AID-PSC179>3.0.CO;2-C

By:

Ježek, Jan;
Velek, Jiří;
Vepřek, Pavel;
Velková, Vlasta;
Trnka, Tomáš;
Pecka, Jaroslav;
Ledvina, Miroslav;
Vondrášek, Jiří;
Písačka, Martin

Publication type:

Article

PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05613-5

By:

Faltejsková, Kateřina;
Vondrášek, Jiří

Publication type:

Article

The LOTUS initiative for open knowledge management in natural products research.

Published in:

eLife, 2022, p. 1, doi. 10.7554/eLife.70780

By:

Rutz, Adriano;
Sorokina, Maria;
Galgonek, Jakub;
Mietchen, Daniel;
Willighagen, Egon;
Gaudry, Arnaud;
Graham, James G.;
Stephan, Ralf;
Page, Roderic;
Vondrášek, Jiří;
Steinbeck, Christoph;
Pauli, Guido F.;
Wolfender, Jean-Luc;
Bisson, Jonathan;
Allard, Pierre-Marie

Publication type:

Article

Increasing Affinity of Interferon-γ Receptor 1 to Interferon-γ by Computer-Aided Design.

Published in:

BioMed Research International, 2013, v. 2013, p. 1, doi. 10.1155/2013/752514

By:

Mikulecký, Pavel;
Černy, Jiří;
Biedermannová, Lada;
Petroková, Hana;
Kuchař, Milan;
Vondrášek, Jiří;
Malý, Petr;
Šebo, Peter;
Schneider, Bohdan

Publication type:

Article

SmSP2: A serine protease secreted by the blood fluke pathogen Schistosoma mansoni with anti-hemostatic properties.

Published in:

PLoS Neglected Tropical Diseases, 2018, v. 12, n. 4, p. 1, doi. 10.1371/journal.pntd.0006446

By:

Leontovyč, Adrian;
Ulrychová, Lenka;
O’Donoghue, Anthony J.;
Vondrášek, Jiří;
Marešová, Lucie;
Hubálek, Martin;
Fajtová, Pavla;
Chanová, Marta;
Jiang, Zhenze;
Craik, Charles S.;
Caffrey, Conor R.;
Mareš, Michael;
Dvořák, Jan;
Horn, Martin

Publication type:

Article

Dispersion Interactions Govern the Strong Thermal Stability of a Protein.

Published in:

Chemistry - A European Journal, 2007, v. 13, n. 32, p. 9022, doi. 10.1002/chem.200700428

By:

Vondrášek, Jiří;
Kubař, Tomáš;
Jenney, Francis E.;
Adams, Michael W. W.;
Kožíšek, Milan;
Černý, Jiří;
Sklenář, Vladimír;
Hobza, Pavel

Publication type:

Article

Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition.

Published in:

PEDS: Protein Engineering, Design & Selection, 2014, v. 27, n. 12, p. 463

By:

Vymětal, Jiří;
Bathula, Sreenivas Reddy;
Černý, Jiří;
Chaloupková, Radka;
Žídek, Lukáš;
Sklenář, Vladimír;
Vondrášek, Jiří

Publication type:

Article

Regioselective Palmitoylation of 9-(2,3-Dihydroxy- propyl)adenine Catalyzed by a Glycopolymer-enzyme Conjugate.

Published in:

Molecules, 2016, v. 21, n. 5, p. 648, doi. 10.3390/molecules21050648

By:

Brabcová, Jana;
Blažek, Jiří;
Krečmerová, Marcela;
Vondrášek, Jiří;
Palomo, Jose M.;
Zarevúcka, Marie

Publication type:

Article

IDSM ChemWebRDF: SPARQLing small-molecule datasets.

Published in:

Journal of Cheminformatics, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13321-021-00515-1

By:

Galgonek, Jakub;
Vondrášek, Jiří

Publication type:

Article

Correction to: Interoperable chemical structure search service.

Published in:

2020

By:

Kratochvíl, Miroslav;
Vondrášek, Jiří;
Galgonek, Jakub

Publication type:

Correction Notice

Interoperable chemical structure search service.

Published in:

Journal of Cheminformatics, 2019, v. 11, n. 1, p. N.PAG, doi. 10.1186/s13321-019-0367-2

By:

Kratochvíl, Miroslav;
Vondrášek, Jiří;
Galgonek, Jakub

Publication type:

Article

Sachem: a chemical cartridge for high-performance substructure search.

Published in:

Journal of Cheminformatics, 2018, v. 10, n. 1, p. 1, doi. 10.1186/s13321-018-0282-y

By:

Kratochvíl, Miroslav;
Vondrášek, Jiří;
Galgonek, Jakub

Publication type:

Article