ASSIST: a fast versatile local structural comparison tool

Abstract Motivation: Structural genomics initiatives are increasingly leading to the determination of the 3D structure of target proteins whose catalytic function is not known. The aim of this work was that of developing a novel versatile tool for searching structural similarity, which allows to predict the catalytic function, if any, of these proteins. Results: The algorithm implemented by the tool is based on local structural comparison to find the largest subset of similar residues between an input protein and known functional sites. The method uses a geometric hashing approach where information related to residue pairs from the input structures is stored in a hash table and then is quickly retrieved during the comparison step. Tests on proteins belonging to different functional classes, done using the Catalytic Site Atlas entries as targets, indicate that the algorithm is able to identify the correct functional class of the input protein in the vast majority of the cases. Availability and implementation: The application was developed in Java SE 6, with a Java Swing Graphic User Interface (GUI). The system can be run locally on any operating system (OS) equipped with a suitable Java Virtual Machine, and is available at the following URL: http://www.computationalbiology.it/software/ASSISTv1.zip. Contact: polticel@uniroma3.it Supplementary information: Supplementary data are available at Bioinformatics online