GenProBiS: web server for mapping of sequence variants to protein binding sites

Nucleic Acids Research
Janez KoncDusanka Janezic

Abstract

Discovery of potentially deleterious sequence variants is important and has wide implications for research and generation of new hypotheses in human and veterinary medicine, and drug discovery. The GenProBiS web server maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein-protein, protein-nucleic acid, protein-compound, and protein-metal ion binding sites. The concept of a protein-compound binding site is understood in the broadest sense, which includes glycosylation and other post-translational modification sites. Binding sites were defined by local structural comparisons of whole protein structures using the Protein Binding Sites (ProBiS) algorithm and transposition of ligands from the similar binding sites found to the query protein using the ProBiS-ligands approach with new improvements introduced in GenProBiS. Binding site surfaces were generated as three-dimensional grids encompassing the space occupied by predicted ligands. The server allows intuitive visual exploration of comprehensively mapped variants, such as human somatic mis-sense mutations related to cancer and non-synonymous single nucleotide polymorphisms from 21 species, within the predicted binding sites regions ...Continue Reading

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Citations

Mar 12, 2019·Expert Opinion on Drug Discovery·Janez Konc
Jul 29, 2021·Journal of Chemical Information and Modeling·Janez KoncDušanka Janežič
Nov 21, 2017·Journal of Chemical Information and Modeling·Marko JukičDušanka Janežič

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