Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms

Background: The number of algorithms available to predict ligand-protein interactions is large and ever-increasing. The number of test cases used to validate these methods is usually small and problem dependent. Recently, several databases have been released for further understanding of protein-ligand interactions, having the Protein Data Bank as backend support. Nevertheless, it appears to be difficult to test docking methods on a large variety of complexes. In this paper we report the development of a new database of protein-ligand complexes tailored for testing of docking algorithms. Methods: Using a new definition of molecular contact, small ligands contained in the 2005 PDB edition were identified and processed. The database was enriched in molecular properties. In particular, an automated typing of ligand atoms was performed. A filtering procedure was applied to select a non-redundant dataset of complexes. Data mining was performed to obtain information on the frequencies of dif...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Luis A. Diago, Persy Morell, Longendri Aguilera, Ernesto Moreno
• Keywords: BMCBI 2007, Database, Docking Algorithms, Ligand Atoms