Annotating Cancer-Related Variants at Protein–Protein Interface with Structure-PPi
A comprehensive analysis of germline and somatic variants requires complex computational approaches that combine next-generation sequencing (NGS)-based omics data with curated annotations from public repositories. Here, we describe Structure-PPi, which facilitates the analysis of cancer-related vari...
| Autores: | , |
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| Tipo de recurso: | capítulo de libro |
| Fecha de publicación: | 2022 |
| País: | España |
| Institución: | Universitat Politècnica de Catalunya (UPC) |
| Repositorio: | UPCommons. Portal del coneixement obert de la UPC |
| Idioma: | inglés |
| OAI Identifier: | oai:upcommons.upc.edu:2117/370820 |
| Acceso en línea: | https://hdl.handle.net/2117/370820 https://dx.doi.org/10.1007/978-1-0716-2293-3_20 |
| Access Level: | acceso abierto |
| Palabra clave: | Protein-protein interactions Protein isoforms 3D structure analysis Protein–protein interactions Rbbt workflows Variants prioritization Cancer mutations Càncer Simulació per ordinador Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica |
| Sumario: | A comprehensive analysis of germline and somatic variants requires complex computational approaches that combine next-generation sequencing (NGS)-based omics data with curated annotations from public repositories. Here, we describe Structure-PPi, which facilitates the analysis of cancer-related variants onto protein 3D structures, interaction interfaces, and other important functional sites (i.e., catalytic, ligand-binding, posttranslational modification). Our approach relies on features extracted from Interactome3D, UniProtKB, InterPro, APPRIS, dbNSFP, and COSMIC databases and provides complementary information to pathogenicity prediction methods. Thus, Structure-PPi helps in the discrimination of false-positive predictions and adds both mechanistic and biological insights into the role of variants in a given cancer. An online version of the tools is available at https://rbbt.bsc.es/StructurePPI/. |
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