Charges from electrostatic potential grid

Most commonly used is certainly the molecular electrostatic potential. It can be derived from any kind of charge distribution. Usually, the MEP is first calculated on a grid and subsequently transformed to the sphere or Gaussian representation. Quite important is the electron density distribution, which closely models the steric occupancy by a molecule. Other approaches utilize artificial fields for physicochemical properties commonly associated with binding, like a field for the hydrophobicity [193] or H-bonding potential [133,194]. 

The next step is to compute the work needed to bring a unit electrostatic charge from infinity to the first point on the grid, and the total work required for this job is a measure of the electrical potential at that particular grid point. The same procedure is then repeated for each of the other grid points, including those which are actually inside the molecule, until the potential has been calculated for every position. 

The descriptors developed to characterize the substrate chemotypes are obtained from a mixture of molecular orbital calculations and GRID probe-pharmacophore recognition. Molecular orbital calculations to compute the substrate s electron density distribution are the first to be performed. All atom charges are determined using the AMI Hamiltonian. Then the computed charges are used to derive a 3D pharmacophore based on the molecular electrostatic potential (MEP) around the substrate molecules. 

SOM FA is a grid-based approach that does not use a probe to determine interaction energies. Instead, each grid point is assigned the shape or —> molecular electrostatic potential (MEP) value (a) shape is represented by binary values equal to 1 for points inside the van der Waals envelope and zero otherwise (b) electrostatic potential values at grid points are calculated from partial charges distributed across the atom centers [Robinson, Winn et al., 1999]. 

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