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Durham University

Department of Biosciences

Profile

Publication details for Prof. Ehmke Pohl

Angles, Renzo, Arenas-Salinas, Mauricio, García, Roberto, Reyes-Suarez, Jose Antonio & Pohl, Ehmke (2020). GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns. BMC Bioinformatics 21(S2): 85.

Author(s) from Durham

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.