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Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0

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  1. 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)

  2. 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)

  3. Article

    Open Access

    Uncovering of cytochrome P450 anatomy by SecStrAnnotator

    Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can he...

    Adam Midlik, Veronika Navrátilová, Taraka Ramji Moturu, Jaroslav Koča in Scientific Reports (2021)

  4. Article

    Open Access

    Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum

    Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localizati...

    Karolina Kubiasová, Juan Carlos Montesinos, Olga Šamajová in Nature Communications (2020)

  5. Chapter

    Concluding Remarks

    This chapter summarizes the purpose and goals of the book.

    Jaroslav Koča, Radka Svobodová Vařeková in Structural Bioinformatics Tools for Drug D… (2016)

  6. Article

    Open Access

    Anatomy of enzyme channels

    Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is know...

    Lukáš Pravda, Karel Berka, Radka Svobodová Vařeková, David Sehnal in BMC Bioinformatics (2014)

  7. 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)