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Nucleic Acids Research Advance Access published online on May 22, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp405
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

MolLoc: a web tool for the local structural alignment of molecular surfaces

Stefano Angaran1, Mary Ellen Bock2, Claudio Garutti1,* and Concettina Guerra1,3

1Department of Information Engineering, University of Padova, Via Gradenigo 6a, Padova, Italy, 2Department of Statistics, Purdue University 250 N. University Street, West Lafayette, IN 47907-2066 and 3College of Computing, Georgia Institute of Technology, Atlanta, GA 30332-0280, USA

*To whom correspondence should be addressed. Tel: +39 049 827 7928; Fax: +39 049 827 7799; Email: garuttic{at}dei.unipd.it

Received February 28, 2009. Revised April 20, 2009. Accepted May 2, 2009.

MolLoc stands for Molecular Local surface comparison, and is a web server for the structural comparison of molecular surfaces. Given two structures in PDB format, the user can compare their binding sites, cavities or any arbitrary residue selection. Moreover, the web server allows the comparison of a query structure with a list of structures. Each comparison produces a structural alignment that maximizes the extension of the superimposition of the surfaces, and returns the pairs of atoms with similar physicochemical properties that are close in space after the superimposition. Based on this subset of atoms sharing similar physicochemical properties a new rototranslation is derived that best superimposes them. MolLoc approach is both local and surface-oriented, and therefore it can be particularly useful when testing if molecules with different sequences and folds share any local surface similarity. The MolLoc web server is available at http://bcb.dei.unipd.it/MolLoc.


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