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Jaroslav Koca
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2020 – today
- 2021
- [j55]Ondrej Schindler
, Tomás Racek
Optimized SQE atomic charges for peptides accessible via a web application. J. Cheminformatics 13(1): 45 (2021) - [j54]Ondrej Schindler
Correction to: Optimized SQE atomic charges for peptides accessible via a web application. J. Cheminformatics 13(1): 52 (2021) - [j53]David Sehnal
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. 49(Webserver-Issue): 431-437 (2021) - 2020
- [j52]David R. Armstrong
PDBe: improved findability of macromolecular structure data in the PDB. Nucleic Acids Res. 48(Database-Issue): D335-D343 (2020) - [j51]Mihaly Varadi
PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 48(Database-Issue): D344-D353 (2020) - [j50]Tomás Racek
Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic Acids Res. 48(Webserver-Issue): W591-W596 (2020) - [j49]David Sehnal, Sebastian Bittrich
BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management. PLoS Comput. Biol. 16(10) (2020)
2010 – 2019
- 2019
- [j48]Vladimír Horský
ValTrendsDB: bringing Protein Data Bank validation information closer to the user. Bioinform. 35(24): 5389-5390 (2019) - 2018
- [j47]Lukás Pravda
ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Res. 46(Database-Issue): D399-D405 (2018) - [j46]Lukás Pravda
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res. 46(Webserver-Issue): W368-W373 (2018) - [c1]David Sehnal, Alexander S. Rose
Mol*: Towards a Common Library and Tools for Web Molecular Graphics. MolVa@EuroVis 2018: 29-33 - 2017
- [j45]Ravi José Tristão Ramos, Allan Cézar de Azevedo Martins
CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. Bioinform. 33(22): 3648-3651 (2017) - 2016
- [j44]Tomás Racek
NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. J. Cheminformatics 8(1): 57:1-57:14 (2016) - 2015
- [j43]Crina-Maria Ionescu, David Sehnal
AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. J. Cheminformatics 7: 50:1-50:13 (2015) - [j42]Stanislav Geidl, Tomás Bouchal
High-quality and universal empirical atomic charges for chemoinformatics applications. J. Cheminformatics 7: 59:1-59:10 (2015) - [j41]Stanislav Geidl, Radka Svobodová Vareková
How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction? J. Chem. Inf. Model. 55(6): 1088-1097 (2015) - [j40]David Sehnal
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. Nucleic Acids Res. 43(Database-Issue): 369-375 (2015) - [j39]David Sehnal
PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Res. 43(Webserver-Issue): W383-W388 (2015) - [j38]Tomás Trnka
Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2. PLoS Comput. Biol. 11(4) (2015) - 2014
- [j37]Lukás Pravda
Anatomy of enzyme channels. BMC Bioinform. 15: 379 (2014) - [j36]Zdenek Kríz, Jan Adam, Jana Mrázková
Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity. J. Comput. Aided Mol. Des. 28(9): 951-960 (2014) - [j35]Deepti Jaiswal Kundu
Consistency of sugar structures and their annotation in the PDB. J. Cheminformatics 6(S-1): 41 (2014) - [j34]Tomás Bouchal, Radka Svobodová Vareková, Tomás Racek, Crina-Maria Ionescu, Stanislav Geidl, Ales Krenek, Jaroslav Koca:
Empirical charges for chemoinformatics applications. J. Cheminformatics 6(S-1): 60 (2014) - [j33]Stanislav Geidl, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca:
QM quality atomic charges for proteins. J. Cheminformatics 6(S-1): 61 (2014) - [j32]Radka Svobodová Vareková
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Res. 42(Webserver-Issue): 227-233 (2014) - 2013
- [j31]Jakub Stepán, Petr Kulhánek, Milan Lenco, Zora Strelcová, Ales Krenek, Jaroslav Koca:
Nemesis - a molecular modeling package. J. Cheminformatics 5(S-1): 12 (2013) - [j30]Radka Svobodová Vareková
Predicting pKa values from EEM atomic charges. J. Cheminformatics 5: 18 (2013) - [j29]David Sehnal, Radka Svobodová Vareková, Karel Berka, Lukás Pravda, Veronika Navrátilová, Pavel Banás, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koca:
MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminformatics 5: 39 (2013) - [j28]Crina-Maria Ionescu, Stanislav Geidl, Radka Svobodová Vareková
Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. J. Chem. Inf. Model. 53(10): 2548-2558 (2013) - 2012
- [j27]Sushil Kumar Mishra
Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models. J. Comput. Chem. 33(29): 2340-2350 (2012) - [j26]Jan Alán, Petr Kulhánek, Jaroslav Koca:
Virtual screening and in silico design of novel inhibitors of bacterial lectins. J. Cheminformatics 4(S-1): 1 (2012) - [j25]Ondrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jan Zidek, Jaroslav Koca:
QSPR designer - employ your own descriptors in the automated QSAR modeling process. J. Cheminformatics 4(S-1): 37 (2012) - [j24]David Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová
SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs. J. Cheminformatics 4(S-1): 59 (2012) - [j23]Deepti Jaiswal Kundu, Radka Svobodová Vareková, Crina-Maria Ionescu, David Sehnal, Jaroslav Koca:
Searching for tunnels of proteins - comparison of approaches and available software tools. J. Cheminformatics 4(S-1): 60 (2012) - [j22]Stanislav Geidl, Roman Beránek, Radka Svobodová Vareková, Tomás Bouchal, Miroslav Brumovský, Michal Kudera, Ondrej Skrehota, Jaroslav Koca:
How the methodology of 3D structure preparation influences the quality of QSPR models? J. Cheminformatics 4(S-1): 61 (2012) - [j21]David Sehnal
SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. J. Chem. Inf. Model. 52(2): 343-359 (2012) - [j20]Sushil Kumar Mishra
In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding. J. Chem. Inf. Model. 52(5): 1250-1261 (2012) - [j19]Karel Berka
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res. 40(Web-Server-Issue): 222-227 (2012) - [j18]Crina-Maria Ionescu, Radka Svobodová Vareková
Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation. PLoS Comput. Biol. 8(6) (2012) - 2011
- [j17]Ondrej Skrehota, Radka Svobodová Vareková
QSPR designer - a program to design and evaluate QSPR models. Case study on pKa prediction. J. Cheminformatics 3(S-1): 16 (2011) - [j16]Radka Svobodová Vareková
Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. J. Chem. Inf. Model. 51(8): 1795-1806 (2011)
2000 – 2009
- 2009
- [j15]Zuzana Jirousková, Radka Svobodová Vareková
Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme. J. Comput. Chem. 30(7): 1174-1178 (2009) - 2008
- [j14]Martin Prokop, Jan Adam, Zdenek Kríz, Michaela Wimmerová
TRITON: a graphical tool for ligand-binding protein engineering. Bioinform. 24(17): 1955-1956 (2008) - [j13]Jan Adam, Zdenek Kríz, Martin Prokop, Michaela Wimmerová
In Silico Mutagenesis and Docking Studies of Pseudomonas aeruginosa PA-IIL Lectin Predicting Binding Modes and Energies. J. Chem. Inf. Model. 48(11): 2234-2242 (2008) - 2006
- [j12]Martin Petrek, Michal Otyepka
CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinform. 7: 316 (2006) - [j11]Radka Svobodová Vareková
Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method. J. Comput. Chem. 27(3): 396-405 (2006) - 2003
- [j10]Jaroslav Koca
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics. J. Comput. Chem. 24(3): 368-378 (2003) - 2000
- [j9]Martin Prokop, Jirí Damborský
TRITON: in silico construction of protein mutants and prediction of their activities. Bioinform. 16(9): 845-846 (2000) - [j8]Michal Cajan, Jirí Damborský
Stability of Complexes of Aromatic Amides with Bromide Anion: Quantitative Structure-Property Relationships. J. Chem. Inf. Comput. Sci. 40(5): 1151-1157 (2000)
1990 – 1999
- 1999
- [j7]Martin Cernohorský, Sofiane Kettou, Jaroslav Koca
VADER: New Software for Exploring Interconversions on Potential Energy Surfaces. J. Chem. Inf. Comput. Sci. 39(4): 705-712 (1999) - 1998
- [j6]Michal Kutý
A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase. 2. Quantum Chemical Study of Complete Reaction Mechanism. J. Chem. Inf. Comput. Sci. 38(4): 736-741 (1998) - 1997
- [j5]Martin Cernohorský, Michal Kutý, Jaroslav Koca:
A Multidimensional Driver for Quantum Chemistry Program MOPAC. Comput. Chem. 21(1): 35-44 (1997) - [j4]Jirí Damborský
A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase: 1. Quantum Chemical Study of the First Reaction Step. J. Chem. Inf. Comput. Sci. 37(3): 562-568 (1997) - 1995
- [j3]Jaroslav Koca
Conformational Analysis and Flexibility of Carbohydrates Using the CICADA Approach with MM3. J. Comput. Chem. 16(3): 296-310 (1995) - 1994
- [j2]Ludek Matyska, Jaroslav Koca
D-CICADA : A Software for Confromational PES Elucidation on Network of Workstations. J. Comput. Chem. 15(9): 937-946 (1994) - 1991
- [j1]Ludek Matyska
MAPOS: a computer program for organic synthesis design based on synthon model of organic chemistry. J. Chem. Inf. Comput. Sci. 31(3): 380-386 (1991)
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last updated on 2024-10-07 21:17 CEST by the dblp team
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