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Nucleic Acids Research Advance Access published online on May 13, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp368
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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

@TOME-2: a new pipeline for comparative modeling of protein–ligand complexes

Jean-Luc Pons and Gilles Labesse*

A.B.C.I.S., CNRS UMR5048—Universités Montpellier 1 & Montpellier II and INSERM U554, 29, Rue de Navacelles 34090 Montpellier Cedex, France

*To whom correspondence should be addressed. Tel: +33 4 67 41 77 12; Fax: +33 3 04 67 41 79 13; Email: labesse{at}cbs.cnrs.fr

Received January 31, 2009. Revised April 17, 2009. Accepted April 24, 2009.

@TOME 2.0 is new web pipeline dedicated to protein structure modeling and small ligand docking based on comparative analyses. @TOME 2.0 allows fold recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation. These tasks are routinely used in sequence analyses for structure prediction. In our pipeline the necessary software is efficiently interconnected in an original manner to accelerate all the processes. Furthermore, we have also connected comparative docking of small ligands that is performed using protein–protein superposition. The input is a simple protein sequence in one-letter code with no comment. The resulting 3D model, protein–ligand complexes and structural alignments can be visualized through dedicated Web interfaces or can be downloaded for further studies. These original features will aid in the functional annotation of proteins and the selection of templates for molecular modeling and virtual screening. Several examples are described to highlight some of the new functionalities provided by this pipeline. The server and its documentation are freely available at http://abcis.cbs.cnrs.fr/AT2/


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