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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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