Small Molecule Atomtyping and Rotatable T orsion assignment

SMART is a tool to setup ligand files for their use with FITTED.

This program automatically identifies and labels the rotatable bonds of the ligands and assigns AMBER atom types. SMART is also used to identify functional groups and assigning descriptors to be used by the REDUCE program.

SMART has originally been reported with FITTED 1.0 and optimized since then.

  • Corbeil C.R., Englebienne P., Moitessier N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0 Journal of Chemical Information and Modeling (2007), 47, 435-449 link

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    Conformational Optimization of Necessary Virtual Enantiomers, Rotamers and Tautomers

    CONVERT is a 2D to 3D small molecules converter. This program:

    1. defines the hybridization states for each atoms of this molecule on the basis of the provided bond orders;
    2. estimates the nitrogen pKa's on the basis of hybridization and aromaticity;
    3. identifies possible tautomers (e.g., imidazole rings) or stereoisomers (including ammonium nitrogens);
    4. creates out-of-plane perturbation at all stereogenic centers;
    5. adds hydrogen atoms;
    6. optimizes the bond lengths, angles, and torsions on the basis of geometric rules and force field parameters;
    7. carries out a conjugate gradient energy-minimization using molecular mechanics;
    8. outputs all of the tautomers/isomers in a multi-mol2 file.

    CONVERT has originally been reported with the FORECASTER platform and optimized since then.

  • Therrien E., Englebienne P., Arrowsmith A.G., Mendoza-Sanchez R., Corbeil C.R., Weill N., Campagna-Slater V., Moitessier N. Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulatorswith FORECASTER, a novel platform for drug discovery Journal of Chemical Information and Modeling (2012), 52, 210-224 link

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    Hyperconjugation for Torsional Energy Quantification

    H-TEQ is a method to derive torsion parameters for small molecules. These force field parameters do not rely on atom types

    and make uses of atomic properties such as electronegativity to estimate these parameters.

    The second version of this method just came out in the litterature.

  • Liu Z., Barigye S. J., Shahamat M., Labute P., Moitessier N. Atom Types Independent Molecular Mechanics Method for Predicting the Conformational Energy of Small Molecules Journal of Chemical Information and Modeling (2018), ASAP link

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