Radka Svobodová Vareková

Orcid: 0000-0002-3840-8760

  • Masaryk University Brno, Czech Republic

According to our database1, Radka Svobodová Vareková authored at least 49 papers between 2006 and 2023.

Collaborative distances:



In proceedings 
PhD thesis 


Online presence:

On csauthors.net:


αCharges: partial atomic charges for AlphaFold structures in high quality.
Nucleic Acids Res., July, 2023

Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations.
Nucleic Acids Res., July, 2023

Onedata4Sci: Life science data management solution based on Onedata.
CoRR, 2023

PDBe-KB: collaboratively defining the biological context of structural data.
Nucleic Acids Res., 2022

OverProt: secondary structure consensus for protein families.
Bioinform., 2022

CATH: increased structural coverage of functional space.
Nucleic Acids Res., 2021

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.
Nucleic Acids Res., 2021

Correction to: Optimized SQE atomic charges for peptides accessible via a web application.
J. Cheminformatics, 2021

Optimized SQE atomic charges for peptides accessible via a web application.
J. Cheminformatics, 2021

2DProts: database of family-wide protein secondary structure diagrams.
Bioinform., 2021

BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management.
PLoS Comput. Biol., 2020

PDBe-KB: a community-driven resource for structural and functional annotations.
Nucleic Acids Res., 2020

Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges.
Nucleic Acids Res., 2020

PDBe: improved findability of macromolecular structure data in the PDB.
Nucleic Acids Res., 2020

ValTrendsDB: bringing Protein Data Bank validation information closer to the user.
Bioinform., 2019

ChannelsDB: database of biomacromolecular tunnels and pores.
Nucleic Acids Res., 2018

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).
Nucleic Acids Res., 2018

Lesson Development for Open Source Software Best Practices Adoption.
Proceedings of the 14th IEEE International Conference on e-Science, 2018

Four simple recommendations to encourage best practices in research software.
F1000Research, 2017

Tools and data services registry: a community effort to document bioinformatics resources.
Nucleic Acids Res., 2016

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges.
J. Cheminformatics, 2016

Top 10 metrics for life science software good practices.
F1000Research, 2016

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.
Nucleic Acids Res., 2015

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank.
Nucleic Acids Res., 2015

How Does the Methodology of 3D Structure Preparation Influence the Quality of p<i>K</i><sub>a</sub> Prediction?
J. Chem. Inf. Model., 2015

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules.
J. Cheminformatics, 2015

High-quality and universal empirical atomic charges for chemoinformatics applications.
J. Cheminformatics, 2015

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.
Nucleic Acids Res., 2014

Consistency of sugar structures and their annotation in the PDB.
J. Cheminformatics, 2014

QM quality atomic charges for proteins.
J. Cheminformatics, 2014

Empirical charges for chemoinformatics applications.
J. Cheminformatics, 2014

Anatomy of enzyme channels.
BMC Bioinform., 2014

Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method.
J. Chem. Inf. Model., 2013

Predicting pKa values from EEM atomic charges.
J. Cheminformatics, 2013

MOLE 2.0: advanced approach for analysis of biomacromolecular channels.
J. Cheminformatics, 2013

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation.
PLoS Comput. Biol., 2012

MOLE<i>online</i> 2.0: interactive web-based analysis of biomacromolecular channels.
Nucleic Acids Res., 2012

SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs.
J. Chem. Inf. Model., 2012

QSPR designer - employ your own descriptors in the automated QSAR modeling process.
J. Cheminformatics, 2012

SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs.
J. Cheminformatics, 2012

Searching for tunnels of proteins - comparison of approaches and available software tools.
J. Cheminformatics, 2012

How the methodology of 3D structure preparation influences the quality of QSPR models?
J. Cheminformatics, 2012

Predicting p<i>K</i><sub>a</sub> Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes.
J. Chem. Inf. Model., 2011

QSPR designer - a program to design and evaluate QSPR models. Case study on pK<sub>a</sub> prediction.
J. Cheminformatics, 2011

Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme.
J. Comput. Chem., 2009

Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO).
J. Chem. Inf. Model., 2008

www.rnaworkbench.com: A new program for analyzing RNA interference.
Comput. Methods Programs Biomed., 2008

Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins.
J. Chem. Inf. Model., 2007

Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method.
J. Comput. Chem., 2006