Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method. - Radka Svobodová Vareková; Jaroslav Koca (J. Comput. Chem., 2006)

Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins. - Ivan Baran; Radka Svobodová Vareková; Laavanya Parthasarathi; Simon Suchomel; Fergal P. Casey; Denis C. Shields (J. Chem. Inf. Model., 2007)

www.rnaworkbench.com: A new program for analyzing RNA interference. - Radka Svobodová Vareková; Ivan Bradác; Martin Plchút; Michal Skrdla; Michael Wacenovsky; Helmuth Mahr; Georg Mayer; Herbert Tanner; Hermann Brugger; Josef Withalm; Peter Lederer; Heinrich J. Huber; et al. (Comput. Methods Programs Biomed., 2008)

Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO). - Fergal P. Casey; Norman E. Davey; Ivan Baran; Radka Svobodová Vareková; Denis C. Shields (J. Chem. Inf. Model., 2008)

Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme. - Zuzana Jirousková; Radka Svobodová Vareková; Jakub Vanek; Jaroslav Koca (J. Comput. Chem., 2009)

QSPR designer - a program to design and evaluate QSPR models. Case study on pKa prediction. - Ondrej Skrehota; Radka Svobodová Vareková; Stanislav Geidl; Michal Kudera; David Sehnal; Crina-Maria Ionescu; Jaroslav Koca (J. Cheminformatics, 2011)

Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. - Radka Svobodová Vareková; Stanislav Geidl; Crina-Maria Ionescu; Ondrej Skrehota; Michal Kudera; David Sehnal; Tomás Bouchal; Ruben Abagyan; Heinrich J. Huber; Jaroslav Koca (J. Chem. Inf. Model., 2011)

How the methodology of 3D structure preparation influences the quality of QSPR models? - Stanislav Geidl; Roman Beránek; Radka Svobodová Vareková; Tomás Bouchal; Miroslav Brumovský; Michal Kudera; Ondrej Skrehota; Jaroslav Koca (J. Cheminformatics, 2012)

Searching for tunnels of proteins - comparison of approaches and available software tools. - Deepti Jaiswal Kundu; Radka Svobodová Vareková; Crina-Maria Ionescu; David Sehnal; Jaroslav Koca (J. Cheminformatics, 2012)

SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs. - David Sehnal; Radka Svobodová Vareková; Heinrich J. Huber; Stanislav Geidl; Crina-Maria Ionescu; Michaela Wimmerová; Jaroslav Koca (J. Cheminformatics, 2012)

QSPR designer - employ your own descriptors in the automated QSAR modeling process. - Ondrej Skrehota; Radka Svobodová Vareková; Stanislav Geidl; Michal Kudera; David Sehnal; Crina-Maria Ionescu; Jan Zidek; Jaroslav Koca (J. Cheminformatics, 2012)

SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. - David Sehnal; Radka Svobodová Vareková; Heinrich J. Huber; Stanislav Geidl; Crina-Maria Ionescu; Michaela Wimmerová; Jaroslav Koca (J. Chem. Inf. Model., 2012)

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. - Karel Berka; Ondrej Hanák; David Sehnal; Pavel Banás; Veronika Navrátilová; Deepti Jaiswal Kundu; Crina-Maria Ionescu; Radka Svobodová Vareková; Jaroslav Koca; Michal Otyepka (Nucleic Acids Res., 2012)

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation. - Crina-Maria Ionescu; Radka Svobodová Vareková; Jochen H. M. Prehn; Heinrich J. Huber; Jaroslav Koca (PLoS Comput. Biol., 2012)

MOLE 2.0: advanced approach for analysis of biomacromolecular channels. - David Sehnal; Radka Svobodová Vareková; Karel Berka; Lukás Pravda; Veronika Navrátilová; Pavel Banás; Crina-Maria Ionescu; Michal Otyepka; Jaroslav Koca (J. Cheminformatics, 2013)

Predicting pKa values from EEM atomic charges. - Radka Svobodová Vareková; Stanislav Geidl; Crina-Maria Ionescu; Ondrej Skrehota; Tomás Bouchal; David Sehnal; Ruben Abagyan; Jaroslav Koca (J. Cheminformatics, 2013)

Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. - Crina-Maria Ionescu; Stanislav Geidl; Radka Svobodová Vareková; Jaroslav Koca (J. Chem. Inf. Model., 2013)

Anatomy of enzyme channels. - Lukás Pravda; Karel Berka; Radka Svobodová Vareková; David Sehnal; Pavel Banás; Roman A. Laskowski; Jaroslav Koca; Michal Otyepka (BMC Bioinform., 2014)

Empirical charges for chemoinformatics applications. - Tomás Bouchal; Radka Svobodová Vareková; Tomás Racek; Crina-Maria Ionescu; Stanislav Geidl; Ales Krenek; Jaroslav Koca (J. Cheminformatics, 2014)

QM quality atomic charges for proteins. - Stanislav Geidl; Crina-Maria Ionescu; Radka Svobodová Vareková; Jaroslav Koca (J. Cheminformatics, 2014)

Consistency of sugar structures and their annotation in the PDB. - Deepti Jaiswal Kundu; David Sehnal; Radka Svobodová Vareková; Crina-Maria Ionescu; Jaroslav Koca (J. Cheminformatics, 2014)

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. - Radka Svobodová Vareková; Deepti Jaiswal Kundu; David Sehnal; Crina-Maria Ionescu; Stanislav Geidl; Lukás Pravda; Vladimír Horský; Michaela Wimmerová; Jaroslav Koca (Nucleic Acids Res., 2014)

High-quality and universal empirical atomic charges for chemoinformatics applications. - Stanislav Geidl; Tomás Bouchal; Tomás Racek; Radka Svobodová Vareková; Václav Hejret; Ales Krenek; Ruben Abagyan; Jaroslav Koca (J. Cheminformatics, 2015)

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. - Crina-Maria Ionescu; David Sehnal; Francesco L. Falginella; Purbaj Pant; Lukás Pravda; Tomás Bouchal; Radka Svobodová Vareková; Stanislav Geidl; Jaroslav Koca (J. Cheminformatics, 2015)

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction? - Stanislav Geidl; Radka Svobodová Vareková; Veronika Bendová; Lukás Petrusek; Crina-Maria Ionescu; Zdenek Jurka; Ruben Abagyan; Jaroslav Koca (J. Chem. Inf. Model., 2015)

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. - David Sehnal; Lukás Pravda; Radka Svobodová Vareková; Crina-Maria Ionescu; Jaroslav Koca (Nucleic Acids Res., 2015)

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. - David Sehnal; Radka Svobodová Vareková; Lukás Pravda; Crina-Maria Ionescu; Stanislav Geidl; Vladimír Horský; Deepti Jaiswal Kundu; Michaela Wimmerová; Jaroslav Koca (Nucleic Acids Res., 2015)

Top 10 metrics for life science software good practices. - Haydee Artaza; Neil P. Chue Hong; Manuel Corpas; Angel Corpuz; Rob W. W. Hooft; Rafael C. Jiménez; Brane Leskosek; Brett G. Olivier; Jan Stourac; Radka Svobodová Vareková; Thomas Van Parys; Daniel Vaughan (F1000Research, 2016)

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. - Tomás Racek; Jana Pazúriková; Radka Svobodová Vareková; Stanislav Geidl; Ales Krenek; Francesco L. Falginella; Vladimír Horský; Václav Hejret; Jaroslav Koca (J. Cheminformatics, 2016)

Tools and data services registry: a community effort to document bioinformatics resources. - Jon C. Ison; Kristoffer Rapacki; Hervé Ménager; Matús Kalas; Emil Rydza; Piotr Chmura; Christian Anthon; Niall Beard; Karel Berka; Dan M. Bolser; Tim Booth; Anthony Bretaudeau; et al. (Nucleic Acids Res., 2016)

Four simple recommendations to encourage best practices in research software. - Rafael C. Jiménez; Mateusz Kuzak; Monther Alhamdoosh; Michelle Barker; Bérénice Batut; Mikael Borg; Salvador Capella-Gutiérrez; Neil P. Chue Hong; Martin Cook; Manuel Corpas; Madison Flannery; Leyla J. García; et al. (F1000Research, 2017)

Lesson Development for Open Source Software Best Practices Adoption. - Mateusz Kuzak; Jen Harrow; Rafael C. Jiménez; Paula Andrea Martínez; Fotis E. Psomopoulos; Radka Svobodová Vareková; Allegra Via (eScience, 2018)

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). - Lukás Pravda; David Sehnal; Dominik Tousek; Veronika Navrátilová; Václav Bazgier; Karel Berka; Radka Svobodová Vareková; Jaroslav Koca; Michal Otyepka (Nucleic Acids Res., 2018)

ChannelsDB: database of biomacromolecular tunnels and pores. - Lukás Pravda; David Sehnal; Radka Svobodová Vareková; Veronika Navrátilová; Dominik Tousek; Karel Berka; Michal Otyepka; Jaroslav Koca (Nucleic Acids Res., 2018)

ValTrendsDB: bringing Protein Data Bank validation information closer to the user. - Vladimír Horský; Veronika Bendová; Dominik Tousek; Jaroslav Koca; Radka Svobodová Vareková (Bioinform., 2019)

PDBe: improved findability of macromolecular structure data in the PDB. - David R. Armstrong; John M. Berrisford; Matthew J. Conroy; Aleksandras Gutmanas; Stephen Anyango; Preeti Choudhary; Alice R. Clark; Jose M. Dana; Mandar S. Deshpande; Roisin Dunlop; Paul J. Gane; Romana Gáborová; et al. (Nucleic Acids Res., 2020)

Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. - Tomás Racek; Ondrej Schindler; Dominik Tousek; Vladimír Horský; Karel Berka; Jaroslav Koca; Radka Svobodová Vareková (Nucleic Acids Res., 2020)

PDBe-KB: a community-driven resource for structural and functional annotations. - Mihaly Varadi; John M. Berrisford; Mandar S. Deshpande; Sreenath Nair; Aleksandras Gutmanas; David R. Armstrong; Lukás Pravda; Bissan Al-Lazikani; Stephen Anyango; Geoffrey J. Barton; Karel Berka; Tom L. Blundell; et al. (Nucleic Acids Res., 2020)

BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management. - David Sehnal; Sebastian Bittrich; Sameer Velankar; Jaroslav Koca; Radka Svobodová Vareková; Stephen K. Burley; Alexander S. Rose (PLoS Comput. Biol., 2020)

2DProts: database of family-wide protein secondary structure diagrams. - Ivana Hutarová Vareková; Jan Hutar; Adam Midlik; Vladimír Horský; Eva Hladká; Radka Svobodová Vareková; Karel Berka (Bioinform., 2021)

Optimized SQE atomic charges for peptides accessible via a web application. - Ondrej Schindler; Tomás Racek; Aleksandra Marsavelski; Jaroslav Koca; Karel Berka; Radka Svobodová Vareková (J. Cheminformatics, 2021)

Correction to: Optimized SQE atomic charges for peptides accessible via a web application. - Ondrej Schindler; Tomás Racek; Aleksandra Marsavelski; Jaroslav Koca; Karel Berka; Radka Svobodová Vareková (J. Cheminformatics, 2021)

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. - David Sehnal; Sebastian Bittrich; Mandar S. Deshpande; Radka Svobodová Vareková; Karel Berka; Václav Bazgier; Sameer Velankar; Stephen K. Burley; Jaroslav Koca; Alexander S. Rose (Nucleic Acids Res., 2021)

CATH: increased structural coverage of functional space. - Ian Sillitoe; Nicola Bordin; Natalie L. Dawson; Vaishali P. Waman; Paul Ashford; Harry M. Scholes; Camilla S. M. Pang; Laurel Woodridge; Clemens Rauer; Neeladri Sen; Mahnaz Abbasian; Sean Le Cornu; et al. (Nucleic Acids Res., 2021)

OverProt: secondary structure consensus for protein families. - Adam Midlik; Ivana Hutarová Vareková; Jan Hutar; Aliaksei Chareshneu; Karel Berka; Radka Svobodová Vareková (Bioinform., 2022)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)

Onedata4Sci: Life science data management solution based on Onedata. - Tomás Svoboda; Tomás Racek; Josef Handl; Jozef Sabo; Adrián Rosinec; Lukasz Opiola; Wojciech Jesionek; Milan Esner; Markéta Pernisová; Natallia Madzia Valasevich; Ales Krenek; Radka Svobodová Vareková (CoRR, 2023)

Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. - Aliaksei Chareshneu; Adam Midlik; Crina-Maria Ionescu; Alexander S. Rose; Vladimír Horský; Alessio Cantara; Radka Svobodová Vareková; Karel Berka; David Sehnal (Nucleic Acids Res., 2023)

αCharges: partial atomic charges for AlphaFold structures in high quality. - Ondrej Schindler; Karel Berka; Alessio Cantara; Ales Krenek; Dominik Tichý; Tomás Racek; Radka Svobodová Vareková (Nucleic Acids Res., 2023)