POOL server: machine learning application for functional site prediction in proteins

• DOI: 10.1093/bioinformatics/bts321
• Publication Date: 2012-06-04T14:09:02Z
• Authors: Srinivas Somarowthu; Mary Jo Ondrechen
• Keywords: 0301 basic medicine; Applications Note; Internet; 03 medical and health sciences; Artificial Intelligence; Static Electricity; Computational Biology; Proteins; Software; Protein Structure, Tertiary

Abstract Summary: We present an automated web server for partial order optimum likelihood (POOL), a machine learning application that combines computed electrostatic and geometric information for high-performance prediction of catalytic residues from 3D structures. Input features consist of THEMATICS electrostatics data and pocket information from ConCavity. THEMATICS measures deviation from typical, sigmoidal titration behavior to identify functionally important residues and ConCavity identifies binding pockets by analyzing the surface geometry of protein structures. Both THEMATICS and ConCavity (structure only) do not require the query protein to have any sequence or structure similarity to other proteins. Hence, POOL is applicable to proteins with novel folds and engineered proteins. As an additional option for cases where sequence homologues are available, users can include evolutionary information from INTREPID for enhanced accuracy in site prediction. Availability: The web site is free and open to all users with no login requirements at http://www.pool.neu.edu. Contact: [e-mail] Supplementary Information: Supplementary data are available at Bioinformatics online.