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GenProBiS: web server for mapping of sequence variants to protein binding sites
Janez Konc1,2, Blaz Skrlj1, Nika Erzen1
1National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
Nucleic Acids Research
|May 13, 2017
Summary
The GenProBiS web server maps genetic variants to protein structures and binding sites, aiding drug discovery and medical research. It helps identify potentially harmful mutations within protein interaction regions.
Area of Science:
- Biochemistry
- Bioinformatics
- Structural Biology
Background:
- Identifying deleterious sequence variants is crucial for advancing human and veterinary medicine and drug discovery.
- Understanding variant impact requires mapping them to protein structures and functional sites.
- Existing tools may lack comprehensive mapping to diverse protein binding interactions.
Purpose of the Study:
- To introduce the GenProBiS web server for mapping sequence variants to protein structures and binding sites.
- To provide a tool for exploring variants in relation to protein-protein, protein-nucleic acid, protein-compound, and protein-metal ion interactions.
- To facilitate hypothesis generation in medicine and drug discovery by visualizing variant locations within functional regions.
Main Methods:
- Utilized the Protein Binding Sites (ProBiS) algorithm for local structural comparisons to define binding sites.
- Employed the ProBiS-ligands approach for ligand transposition to identify binding sites on query proteins.
- Generated 3D grids representing binding site surfaces and integrated with WebGL for visualization.
- Mapped human somatic mutations and non-synonymous single nucleotide polymorphisms from 21 species to approximately 80,000 Protein Data Bank (PDB) structures.
Main Results:
- The GenProBiS server successfully maps sequence variants to various protein binding sites, including post-translational modification sites.
- It provides intuitive visual exploration of variants, such as cancer-related mutations, within predicted binding regions.
- The server integrates data from ~80,000 PDB structures, offering broad applicability.
Conclusions:
- GenProBiS offers a valuable resource for researchers by linking genetic variants to specific functional regions on protein structures.
- The tool enhances the discovery of potentially deleterious variants and supports hypothesis generation in biomedical research.
- The web server is freely accessible, promoting wider use in medicine and drug discovery.
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