Publications

2014

• Anatomy of Enzyme Channels

  PRAVDA Lukáš BERKA Karel SVOBODOVÁ VAŘEKOVÁ Radka SEHNAL David BANÁŠ Pavel ROMAN A Laskowski KOČA Jaroslav OTYEPKA Michal

  Article in Periodical

  BMC Bioinformatics, year: 2014, volume: 15, edition: november, DOI

• MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes

  SVOBODOVÁ VAŘEKOVÁ Radka JAISWAL Deepti SEHNAL David IONESCU Crina-Maria GEIDL Stanislav PRAVDA Lukáš HORSKÝ Vladimír WIMMEROVÁ Michaela KOČA Jaroslav

  Article in Periodical

  Nucleic Acids Research, year: 2014, volume: 42, edition: W1, DOI

2013

• MOLE 2.0: advanced approach for analysis of biomacromolecular channels

  SEHNAL David SVOBODOVÁ VAŘEKOVÁ Radka BERKA Karel PRAVDA Lukáš NAVRÁTILOVÁ Veronika BANÁŠ Pavel IONESCU Crina-Maria OTYEPKA Michal KOČA Jaroslav

  Article in Periodical

  Journal of Cheminformatics, year: 2013, volume: 5, edition: 39, DOI

• Predicting pKa values from EEM atomic charges

  SVOBODOVÁ VAŘEKOVÁ Radka GEIDL Stanislav IONESCU Crina-Maria SKŘEHOTA Ondřej BOUCHAL Tomáš SEHNAL David ABAGYAN Ruben A. KOČA Jaroslav

  Article in Periodical

  Journal of Cheminformatics, year: 2013, volume: 5, edition: 18, DOI

• Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method

  IONESCU Crina-Maria GEIDL Stanislav SVOBODOVÁ VAŘEKOVÁ Radka KOČA Jaroslav

  Article in Periodical

  Journal of Chemichal Information a Modeling, year: 2013, volume: 53, edition: 10, DOI

2012

• Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation

  IONESCU Crina-Maria SVOBODOVÁ VAŘEKOVÁ Radka PREHN Jochen HM HUBER Heinrich J KOČA Jaroslav

  Article in Periodical

  PLoS Computational Biology, year: 2012, volume: 8, edition: 6, DOI

• MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels

  BERKA Karel HANÁK Ondřej SEHNAL David BANÁŠ Pavel NAVRÁTILOVÁ Veronika JAISWAL Deepti IONESCU Crina-Maria SVOBODOVÁ VAŘEKOVÁ Radka KOČA Jaroslav OTYEPKA Michal

  Article in Periodical

  Nucleic Acids Research, year: 2012, volume: 40, edition: W1, DOI

• SiteBinder: An improved approach for comparing multiple protein structural motifs

  SEHNAL David SVOBODOVÁ VAŘEKOVÁ Radka HUBER Heinrich J. GEIDL Stanislav IONESCU Crina-Maria WIMMEROVÁ Michaela KOČA Jaroslav

  Article in Periodical

  Journal of Chemical Information and Modeling, year: 2012, volume: 52, edition: 2, DOI

2011

• Predicting pK(a) values of substituted phenols from atomic charges: Comparison of different quantum mechanical methods and charge distribution schemes

  SVOBODOVÁ VAŘEKOVÁ Radka GEIDL Stanislav IONESCU Crina-Maria SKŘEHOTA Ondřej KUDERA Michal SEHNAL David BOUCHAL Tomáš ABAGYAN Ruben A. HUBER Heinrich J. KOČA Jaroslav

  Article in Periodical

  Journal of Chemical Information and Modeling, year: 2011, volume: 51, edition: 8

2008

• Software news and updates: Electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme

  JIROUŠKOVÁ Zuzana SVOBODOVÁ VAŘEKOVÁ Radka VANĚK Jakub KOČA Jaroslav

  Article in Periodical

  Journal of Computational Chemistry, year: 2008, volume: 2009, edition: 30