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Nucleic Acids Research Advance Access originally published online on May 7, 2007
Nucleic Acids Research 2007 35(Web Server issue):W568-W572; doi:10.1093/nar/gkm289
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W568-W572
© 2007 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.

Articles

Frog: a FRee Online druG 3D conformation generator

T. Bohme Leite1, D. Gomes1, M.A. Miteva2, J. Chomilier3, B.O. Villoutreix2 and P. Tufféry1,*

1Equipe de Bioinformatique Génomique et Moléculaire, INSERM UMR 726, Université Paris 7, case 7113, 2, place Jussieu, 75251 Paris cedex 05, 2Equipe de Bioinformatique Structurale et Drug Design - INSERM U648 - Université Paris 5, 45 rue des Sts Peres, 75006 Paris and 3Département de Biologie Structurale - CNRS UMR 7590 - Universités Paris 6 et 7, Université Pierre et Marie CURIE - 4 place Jussieu - case postale 115 - 75252 Paris cedex 05, France

*To whom correspondence should be addressed. Tel: +331 44 277733; Fax: +331 43 263830; Email: tuffery{at}ebgm.jussieu.fr

Received January 31, 2007. Revised April 6, 2007. Accepted April 12, 2007.

In silico screening methods based on the 3D structures of the ligands or of the proteins have become an essential tool to facilitate the drug discovery process. To achieve such process, the 3D structures of the small chemical compounds have to be generated. In addition, for ligand-based screening computations or hierarchical structure-based screening projects involving a rigid-body docking step, it is necessary to generate multi-conformer 3D models for each input ligand to increase the efficiency of the search. However, most academic or commercial compound collections are delivered in 1D SMILES (simplified molecular input line entry system) format or in 2D SDF (structure data file), highlighting the need for free 1D/2D to 3D structure generators. Frog is an on-line service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions. Given the atomic constitution of the molecules and connectivity information, Frog can identify the different unambiguous isomers corresponding to each compound, and generate single or multiple low-to-medium energy 3D conformations, using an assembly process that does not presently consider ring flexibility. Tests show that Frog is able to generate bioactive conformations close to those observed in crystallographic complexes. Frog can be accessed at http://bioserv.rpbs.jussieu.fr/Frog.html.


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