RECCR Rensselaer Exploratory Center for Cheminformatics Research


Molecular Simulation-Based Descriptors


Co-PI: Shekhar Garde

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Molecular Simulation-Based Descriptors

Co-Investigator: Shekhar Garde

Assistant Professor, Chemical and Biological Engineering, Rensselaer Polytechnic Institute


Simulation-derived Hydration-based descriptors: Statistical analysis of the dynamic behavior of water distributions solvating large and small molecules was used to create a set of regional property descriptors found to generate better ligand binding and QSPR models than field- or atom-based electrostatic potential, HBDA or lipophilicity descriptors. Initial data shows that models of molecular behavior created using these features required fewer descriptors and were more interpretable by bench chemists than models built using traditional 3D descriptors.

Interactions of proteins and other biomolecules with water influence the properties of those vicinal water molecules. This effect is especially pronounced locally, especially in the first hydration shell. We quantify the hydration shell properties by calculating spatially resolved (i) average local water density, (ii) water density fluctuations, (iii) local water orientations, (iv) electron density profile due to water packing and orientations (i.e., polarization), (v) electrostatic potential on protein surface induced by the vicinal water structuring, and (vi) dynamics of local water.

This local property information can be projected (Figure 1) on to a triangulated surface of the molecule of interest and forms input to descriptor generation algorithms based on surface properties.

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