GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns

Angles, Renzo; Arenas-Salinas, Mauricio; Garcia, Roberto; Reyes-Suarez, Jose Antonio; Pohl, Ehmke

Abstract

Background In the field of protein engineering and biotechnology, the discovery and characterization of structural patterns is highly relevant as these patterns can give fundamental insights into protein-ligand interaction and protein function. This paper presents GSP4PDB, a bioinformatics web tool that enables the user to visualize, search and explore protein-ligand structural patterns within the entire Protein Data Bank. Results We introduce the notion of graph-based structural pattern (GSP) as an abstract model for representing protein-ligand interactions. A GSP is a graph where the nodes represent entities of the protein-ligand complex (amino acids and ligands) and the edges represent structural relationships (e.g. distances ligand - amino acid). The novel feature of GSP4PDB is a simple and intuitive graphical interface where the user can "draw" a GSP and execute its search in a relational database containing the structural data of each PDB entry. The results of the search are displayed using the same graph-based representation of the pattern. The user can further explore and analyse the results using a wide range of filters, or download their related information for external post-processing and analysis. Conclusions GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction.

Más información

Título según WOS: GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns
Título según SCOPUS: GSP4PDB: A web tool to visualize, search and explore protein-ligand structural patterns
Título de la Revista: BMC BIOINFORMATICS
Volumen: 21
Editorial: BMC
Fecha de publicación: 2020
Idioma: English
DOI:

10.1186/s12859-020-3352-x

Notas: ISI, SCOPUS