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    TOOLKIT DEVELOPMENT PROGRAM

    Omega TK

    Omega TK offers the same features as the OMEGA application for conformer generation.

    Omega TK was designed for use with the large libraries required for computer-aided drug design. It generates multi-conformer structure databases with high speed and reliability.

    Omega TK performs rapid conformational expansion of drug-like molecules, yielding a throughput of tens of thousands of compounds per day per processor.

    Please refer to the OMEGA product page for additional details.

    For even more information on Omega TK, check out the link below:

    Documentation
    Omega toolkit.
    OMEGA provides 2 different methods for conformation generation: torsion driving and distance geometry.

    Modeling

    The Modeling suite of toolkits provides the core functionality underlying OpenEye's defining principle that shape & electrostatics are the two fundamental descriptors determining intermolecular interactions. Many of the toolkits in the Modeling suite are directly associated with specific OpenEye applications and can, therefore, be used to create new or extend existing functionality associated with those applications.

    • OEChem TK Core chemistry handling and representation as well as molecule file I/O
    • OEDocking TK Molecular docking and scoring
    • Omega TK Conformer generation
    • Shape TK 3D shape description, optimization, and overlap
    • SiteHopper TK Rapid Comparison of Protein Binding Sites
    • Spicoli TK Surface generation, manipulation, and interrogation
    • Spruce TK Protein preparation and modeling
    • Szybki TK General purpose optimization with MMFF94
    • Szmap TK Understanding water interactions in a binding site
    • Zap TK Calculate Poisson-Boltzmann electrostatic potentials

    Cheminformatics

    The Cheminformatics suite of toolkits provides the core foundation upon which all of the OpenEye applications and remaining toolkits are built. The Cheminformatics suite is a collection of seven individual yet interdependent toolkits that are described in the table below.

    • FastROCS™ TK Real-time shape similarity for virtual screening, lead hopping & shape clustering
    • OEChem TK Core chemistry handling and representation as well as molecule file I/O
    • OEDepict TK 2D Molecule rendering and depiction
    • Grapheme™ TK Advanced molecule rendering and report generation
    • GraphSim TK 2D molecular similarity (e.g. fingerprints)
    • Lexichem TK name-to-structure, structure-to-name, foreign language translation
    • Quacpac TK Tautomer enumeration and charge assignment
    • MedChem TK Matched molecular pair analysis, fragmentation utilities, and molecular complexity metrics

    References

    1. Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database, Hawkins, P.C.D., Skillman, A.G., Nicholls, A., J. Med. Chem., 2007, 50, 74.
    2. Conformer generation with OMEGA: Learning from the dataset and analysis of failures, Hawkins, P.C.D., Nicholls, A.N., J. Chem. Inf. Model., 2012, 52, 2919.
    3. Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding, E. Perola and P.S. Charifson. J. Med. Chem. 2004,47, 2499-2510.
    4. Comparison of Conformational Analysis Techniques to Generate Pharmacophore Hypotheses Using Catalyst, R. Kristam, V.J. Gillet, R.A. Lewis and D. Thorner. J. Chem. Inf. Model.2005, 45, 461-476.

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