A Graph-Based Approach for Querying Protein-Ligand Structural Patterns

In the context of protein engineering and biotechnology, the discovery and characterization of structural patterns is very relevant as it can give fundamental insights about protein structures. In this paper we present GSP4PDB, a bioinformatics web tool that lets the users design, search and analyze protein-ligand structural patterns inside the Protein Data Bank (PDB). The novel feature of GSP4PDB is that a protein-ligand structural pattern is graphically designed as a graph such that the nodes represent protein's components and the edges represent structural relationships. The resulting graph pattern is transformed into a SQL query, and executed in a PostgreSQL database system where the PDB data is stored. The results of the search are presented using a textual representation, and the corresponding binding-sites can be visualized using a JSmol interface.