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  1. Article

    Open Access

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

    Deepti Jaiswal, Radka Svobodová Vařeková, Crina-Maria Ionescu in Journal of Cheminformatics (2012)

  2. Article

    Open Access

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

    Ondřej Skřehota, Radka Svobodová Vařeková, Stanislav Geidl in Journal of Cheminformatics (2012)

  3. Article

    Open Access

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

    Stanislav Geidl, Roman Beránek, Radka Svobodová Vařeková in Journal of Cheminformatics (2012)

  4. Article

    Open Access

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

    David Sehnal, Radka Svobodová Vařeková, Heinrich J Huber in Journal of Cheminformatics (2012)

  5. Article

    Open Access

    Virtual screening and in silico design of novel inhibitors of bacterial lectins

    Jan Alán, Petr Kulhánek, Jaroslav Koča in Journal of Cheminformatics (2012)

  6. Article

    Open Access

    Nemesis - a molecular modeling package

    Jakub Štěpán, Petr Kulhánek, Milan Lenčo, Zora Střelcová in Journal of Cheminformatics (2013)

  7. Article

    Open Access

    Predicting pK a values from EEM atomic charges

    The acid dissociation constant p K a is a very important molecular property, and there is a strong interest in the development of reliable and fast methods for p K ...

    Radka Svobodová Vařeková, Stanislav Geidl in Journal of Cheminformatics (2013)

  8. Article

    Open Access

    MOLE 2.0: advanced approach for analysis of biomacromolecular channels

    Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity.

    David Sehnal, Radka Svobodová Vařeková, Karel Berka in Journal of Cheminformatics (2013)

  9. Article

    Open Access

    QM quality atomic charges for proteins

    Stanislav Geidl, Crina-Maria Ionescu in Journal of Cheminformatics (2014)

  10. Article

    Open Access

    Empirical charges for chemoinformatics applications

    Tomáš Bouchal, Radka Svobodová Vařeková, Tomáš Raček in Journal of Cheminformatics (2014)

  11. Article

    Open Access

    Consistency of sugar structures and their annotation in the PDB

    Deepti Jaiswal, David Sehnal, Radka Svobodová Vařeková in Journal of Cheminformatics (2014)

  12. Article

    Open Access

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

    Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites.

    Crina-Maria Ionescu, David Sehnal, Francesco L. Falginella in Journal of Cheminformatics (2015)

  13. Article

    Open Access

    High-quality and universal empirical atomic charges for chemoinformatics applications

    Partial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to the chemical behaviour of molecules. Recently, these charges have become popular in chemoinform...

    Stanislav Geidl, Tomáš Bouchal, Tomáš Raček in Journal of Cheminformatics (2015)

  14. Article

    Open Access

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

    The concept of partial atomic charges was first applied in physical and organic chemistry and was later also adopted in computational chemistry, bioinformatics and chemoinformatics. The electronegativity equal...

    Tomáš Raček, Jana Pazúriková, Radka Svobodová Vařeková in Journal of Cheminformatics (2016)

  15. Article

    Open Access

    Optimized SQE atomic charges for peptides accessible via a web application

    Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity ...

    Ondřej Schindler, Tomáš Raček, Aleksandra Maršavelski in Journal of Cheminformatics (2021)

  16. Article

    Open Access

    Correction to: Optimized SQE atomic charges for peptides accessible via a web application

    A Correction to this paper has been published: https://doi.org/10.1186/s13321-021-00528-w

    Ondřej Schindler, Tomáš Raček, Aleksandra Maršavelski in Journal of Cheminformatics (2021)