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List of works by Radka Svobodová Vařeková

AlphaFind: discover structure similarity across the proteome in AlphaFold DB

scientific article published in 2024

Anatomy of enzyme channels

scientific article

Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges

scientific article published on 13 May 2020

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules

scientific article (publication date: 2015)

BinaryCIF and CIFTools-Lightweight, efficient and extensible macromolecular data management

scientific article published on 19 October 2020

Biomacromolecular Fragments and Patterns

CATH: increased structural coverage of functional space

scientific article published on 25 November 2020

Channel Characteristics

ChannelsDB: database of biomacromolecular tunnels and pores

scientific article published on 3 October 2017

Characterization via Charges

Charge profile analysis reveals that activation of pro-apoptotic regulators Bax and Bak relies on charge transfer mediated allosteric regulation

scientific article

Complete Process of Data Extraction and Analysis

Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods

scientific article published in 2004

Concluding Remarks

Consistency of sugar structures and their annotation in the PDB.

scientific article published on 11 March 2014

Detection and Extraction of Fragments

Detection of Channels

Electronegativity Equalization Method: Parameterization and Validation for Large Sets of Organic, Organohalogene and Organometal Molecule.

scientific article published on 3 July 2007

Empirical charges for chemoinformatics applications.

scientific article published on 11 March 2014

Exercises Solution

Four simple recommendations to encourage best practices in research software

scientific article

High-performance macromolecular data delivery and visualization for the web

scientific article published on 26 November 2020

High-performance macromolecular data delivery and visualization for the web. Corrigendum

scientific article published on 01 January 2021

High-quality and universal empirical atomic charges for chemoinformatics applications

scientific article (publication date: 2015)

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction?

scientific article published on 11 June 2015

How the methodology of 3D structure preparation influences the quality of QSPR models?

scientific article

Identification of potential small molecule peptidomimetics similar to motifs in proteins.

scientific article

Introduction

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data

scientific article published in November 2017

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

scientific article (publication date: 16 August 2013)

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

scientific article

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

scientific article published in July 2018

Mole 2.5 - Tool for Detection and Analysis of Macromolecular Pores and Channels

scholarly article by Karel Berka et al published February 2017 in Biophysical Journal

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

scientific article

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges

scientific article (publication date: 2016)

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

scientific article

PDBsum: Structural summaries of PDB entries

scientific article published on 5 September 2017

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank

scientific article

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

scientific article published in August 2011

Predicting pKa values from EEM atomic charges

scientific article published on 10 April 2013

QM quality atomic charges for proteins.

scientific article published on 11 March 2014

QSPR designer – employ your own descriptors in the automated QSAR modeling process.

scientific article

Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method

scientific article published on 13 September 2013

Searching for tunnels of proteins – comparison of approaches and available software tools.

scientific article

SiteBinder – an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs.

scientific article

SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs

scientific database

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

article

Structural Bioinformatics Databases of General Use

Structural Bioinformatics Tools for Drug Design

SugarSketcher: Quick and Intuitive Online Glycan Drawing

Tools and data services registry: a community effort to document bioinformatics resources

scientific article

Top 10 metrics for life science software good practices

scientific article published on 16 August 2016

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

scientific article published on 11 June 2021

ValTrendsDB: bringing Protein Data Bank validation information closer to the user

scientific article published on 01 December 2019

Validation

book chapter in Structural Bioinformatics Tools for Drug Design (2016)

Validation of ligands in macromolecular structures determined by X-ray crystallography.

scientific article

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank

scientific article

Visualization and Analysis of Protein Structures with LiteMol Suite

scientific article published on 01 January 2020

Web server to identify similarity of amino acid motifs to compounds (SAAMCO).

scientific article

Worldwide Protein Data Bank validation information: usage and trends.

scientific article

siRNA selection criteria--statistical analyses of applicability and significance

scientific article published on 21 May 2007

www.rnaworkbench.com: A new program for analyzing RNA interference

scientific article published on 22 January 2008

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