GRID parametrization

The base theory underpinning TOPP is similar to the FLAP approach, previously described in this chapter. First, atoms in the molecules are classified by the GRID force field parametrization. In this way, atoms are described according... 

Grid generation tools automatic/parametric generation, recovery from error (UNDO facilities)... 

VolSurf descriptors, such as G-WHIM and GRIND, encode information present in molecular interactionfields (MIF) calculated by the GRID force field parametrization [Grivori, Gruciani et al, 2000 Crudani, Grivori et al, 2000 Grudani, Pastor et al, 2000 Mannhold, Berellini et al, 2006]. 

To calculate TOPP descriptors, the atoms of each molecule are first classified by the GRID force field parametrization in four different categories according to their charge and hydrogen bond properties DRY (hydrophobic), DONN (hydrogen-bond donor, HBD), ACPT (hydrogen-bond acceptor, HBA), and DNAC (both HBD and HBA). 

Atoms in molecules are first classified into different pharmacophoric types by the GRID force field parametrization. Features considered are hydrophobicity, hydrogen-bond donor and acceptor capabilities, and charge. Then, all accessible geometries for all the combinations of three or four features are calculated and encoded in the final vector. Fingerprints can be calculated both for ligands and proteins. In small ligands, pharmacophores are defined by triplets or quartets of atoms, vhich have critical interactions with a receptor. 

Consider a general coordinate system (u, v, w) defined by its g(u,v, zu) metrics which typify all implementation issues and the appropriate grid selection. Assuming that all derivatives throughout the formulation will be evaluated with an Mth-order accuracy, the parametric expressions for the spatial and temporal approximants, respectively, are given by... 

Molecular interaction fields can also be generated using GRIN/GRID. This method is especially reliable because it is based on a very careful parametrization of the interaction terms. The parameters are founded from experimental crystallographic data that is, the direction, type and typical strength of a particular interaction are classified according to actual crystals. 

Jadhav, P. and Mantena, P.R. (2007) Parametric optimization of grid-stiffened composite panels for maximizing their performance under transverse loading. Composite Structures, 77, 353-363. 

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