Recently, researchers at the French research institutes INSERM and CNRS developed an online service for converting SMILES string to 3D conformers: "FRee Online druG 3D conformation generator (Frog)". A description of this service was published in T. Bohme Leite, D. Gomes, M.A. Miteva, J. Chomilier, B.O. Villoutreix and P. Tufféry. Nucleic Acids Research, 2007, 35, W568-W572:
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.
On behalf of the OpenBabel project, I am pleased to announce that Dr. Bruno Villoutreix (INSERM, University of Paris 5) and Dr. Pierre Tufféry (INSERM, University of Paris 7) have generously donated their code to OpenBabel. This code will be incorporated into OpenBabel under the GPL in the coming months, making fast and accurate SMILES-to-3D conformer generation available to the open source community for the first time.
The absence of an open source 3D conformer generation algorithm has increasingly become a problem in recent years due to the popularity of SMILES strings for the description of molecular information. Fortunately, this problem has now been solved. Thanks again to all those involved in the development and release of this code.
For further information on Frog, please contact the corresponding author of the Frog paper.
Image credit: gottcha78
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