Frog2: Efficient 3D conformation ensemble generator for small compounds
Open Access
- 5 May 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 38 (Web Server), W622-W627
- https://doi.org/10.1093/nar/gkq325
Abstract
Frog is a web tool dedicated to small compound 3D generation. Here we present the new version, Frog2, which allows the generation of conformation ensembles of small molecules starting from either 1D, 2D or 3D description of the compounds. From a compound description in one of the SMILES, SDF or mol2 formats, the server will return an ensemble of diverse conformers generated using a two stage Monte Carlo approach in the dihedral space. When starting from 1D or 2D description of compounds, Frog2 is capable to detect the sites of ambiguous stereoisomery, and thus to sample different stereoisomers. Frog2 also embeds new energy minimization and ring generation facilities that solve the problem of some missing cycle structures in the Frog1 ring library. Finally, the optimized generator of conformation ensembles in Frog2 results in a gain of computational time permitting Frog2 to be up to 20 times faster that Frog1, while producing satisfactory conformations in terms of structural quality and conformational diversity. The high speed and the good quality of generated conformational ensembles makes it possible the treatment of larger compound collections using Frog2. The server and documentation are freely available at http://bioserv.rpbs.univ-paris-diderot.fr/Frog2.Keywords
This publication has 27 references indexed in Scilit:
- DG-AMMOS: A New tool to generate 3D conformation of small molecules using D istance G eometry and A utomated M olecular M echanics O ptimization for in silico S creeningBMC Chemical Biology, 2009
- Targeted scoring functions for virtual screeningDrug Discovery Today, 2009
- AMMOS: Automated Molecular Mechanics Optimization tool for in silico ScreeningBMC Bioinformatics, 2008
- MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screeningBMC Bioinformatics, 2008
- Protein–protein interaction inhibition (2P2I) combining high throughput and virtual screening: Application to the HIV-1 Nef proteinProceedings of the National Academy of Sciences of the United States of America, 2007
- Frog: a FRee Online druG 3D conformation generatorNucleic Acids Research, 2007
- Database resources of the National Center for Biotechnology InformationNucleic Acids Research, 2006
- FAF-Drugs: free ADME/tox filtering of compound collectionsNucleic Acids Research, 2006
- The Blue Obelisk—Interoperability in Chemical InformaticsJournal of Chemical Information and Modeling, 2006
- Description of several chemical structure file formats used by computer programs developed at Molecular Design LimitedJournal of Chemical Information and Computer Sciences, 1992