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Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst:  A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations

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Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52, A-6020 Innsbruck, Austria, and Inte:Ligand Software-Entwicklungs- und Consulting GmbH, Clemens Maria Hofbauer-Gasse 6, A-2344 Maria Enzersdorf, Austria
Cite this: J. Chem. Inf. Model. 2006, 46, 4, 1848–1861
Publication Date (Web):June 30, 2006
https://doi.org/10.1021/ci060084g
Copyright © 2006 American Chemical Society

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    Abstract

    In continuation of our studies to evaluate the ability of various conformer generators to produce bioactive conformations, we present the extension of our work on the analysis of Catalyst's conformational subsampling algorithm in a comparative evaluation with OpenEye's currently updated tool Omega 2.0. Our study is based on an enhanced test set of 778 drug molecules and pharmacologically relevant compounds extracted from the Protein Data Bank (PDB). We elaborated protocols for two common conformer generation use cases and applied them to both programs:  (i) high-throughput settings for processing large databases and (ii) high-quality settings for binding site exploration or lead structure refinement. While Catalyst is faster in the first case, Omega 2.0 better reproduces the bound ligand conformations from the PDB in less time for the latter case.

     University of Innsbruck.

     Inte:Ligand Software-Entwicklungs- und Consulting GmbH.

    *

     Corresponding author phone:  +43-512-507-5252; fax:  +43-512-507-5269; e-mail:  [email protected].

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    PDB code and SMILES notation of all 778 assessed compounds and two investigated examples of the conformational search depth in addition to Figure 7. This material is available free of charge via the Internet at http://pubs.acs.org.

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