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

BMC Bioinformatics

Jose Antonio Reyes-Suarez¹  Mauricio Arenas-Salinas¹  Ehmke Pohl²  Renzo Angles³  Roberto García⁴ 

[1] Centro de Bioinformática y Simulación Molecular, Universidad de Talca;Department of Chemistry, Durham University;Department of Computer Science, Universidad de Talca;Millennium Institute for Foundational Research on Data;

关键词: PDB;    Protein-ligand interaction;    Structural patterns;    Big data;   

DOI  :  10.1186/s12859-020-3352-x

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown