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    WATER: WHERE IT MATTERS, WHEN IT MATTERS

    Szmap TK

    All protein-ligand binding interactions occur in an aqueous environment, therefore predicting the effects of solvent molecules within the binding site is a necessary step in understanding binding affinity. However, the interactions of protein and ligand together with water molecules can have complex and non-obvious effects, which can complicate and obfuscate a lead optimization campaign.

    The Szmap TK provides the foundation and functionality underlying the SZMAP application that helps modelers and medicinal chemists understand the role of water in molecular interactions such as ligand binding. Using water as a lens, SZMAP can provide the user with insight on critical features of a binding site, predict where and how neighboring waters can influence binding of a ligand, or generate ligand modification hypotheses designed to better exploit specific regions on a binding site.

    The semi-continuum [1, 2] approach used in SZMAP combines one explicit water molecule with robust continuum solvent methods [3], classical statistical mechanics, and thorough sampling plus the ability to analyze specific water orientations.

    For more detailed information on Szmap TK, check out the link below:

    Documentation
    szmap-web-image1
    SZMAP calculations identify significant favorable or unfavorable regions of solvent thermodynamics in the binding site. Dominant water orientations are shown, which often match beneficial functional groups on ligands that bind to the protein.

    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
    • FastROCS™ TK Real-time shape similarity for virtual screening, lead hopping & shape clustering
    • 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 the OpenEye applications and remaining toolkits are built.

    • 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
    • MolProp TK Molecular property calculation and filtering
    • Quacpac TK Tautomer enumeration and charge assignment
    • MedChem TK Matched molecular pair analysis, fragmentation utilities, and molecular complexity metrics

    References

    1. Calculation of the thermodynamic properties of aqueous electrolytes to 1000.degree.C and 5000 bar from a semicontinuum model for ion hydration Tanger, J.C., Pitzer, K.S., J. Phys. Chem. 1989, 93, 4941-4951.
    2. Continuum based calculations of hydration entropies and the hydrophobic effect Rashin, A.A., Bukatin, M.A., J. Phys. Chem. 1991, 95, 2942-2944.
    3. A Smooth Permittivity Function for Poisson-Boltzmann Solvation Methods Grant, J.A., Pickup, B., Nicholls, A., J. Comp. Chem. 2001, 22, 608-640.

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