Molecular GRID force field

The interaction of drug molecules with biological membranes is a three-dimensional (3D) recognition that is mediated by surface properties such as shape, Van der Waals forces, electrostatics, hydrogen bonding, and hydrophobicity. Therefore, the GRID force field [5-7], which is able to calculate energetically favorable interaction sites around a molecule, was selected to produce 3D molecular interaction fields. 

Figure 12.2 The X-ray structure of human UGT2B7 (left) showing the UDPGA-binding site (left), and their molecular interaction fields (right) obtained using GRID force field [21], showing the large cavity and the hydrophilic regions (in blue).

Cruciani, G. and Watson, K.A. Comparative molecular field analysis using GRID force-field and GOLPE variable selection methods in a study of inhibitors of glycogen phosphorylase b. 

Cruciani et al., used a dynamic physicochemical interaction model to evaluate the interaction energies between a water probe and the hydrophilic and hydrophobic regions of the solute with the GRID force field. The VolSurf program was used to generate a PLS model able to predict log Poet [51] from the 3D molecular structure. 

Cmciani, G., Watson, K. Comparative Molecular Field Analysis Using GRID Force Field and GOLPE Variable Selection Methods in a Study of Inhibitors of... 

In principle, any method which is able to produce a molecular interaction field (MIF) could be applied to the characterization of the targets. However, almost exclusively the GRID program [19] has been used. This is due to the size of the problem which excludes the use of standard ah initio or semiempirical methods to produce interaction maps. It also reflects the many successful applications of the GRID force field in the characterization of protein active sites and the interpreta-... 

Sciabola, S., Baroni, M., Carosati, E., Cruciani, G. Recent improvements in the GRID force field. 1. The docking procedure GLUE, poster presented at the 15 Eur. Symp. QSAR Molecular Modelling, Istanbul, Turkey 2004. 

The most common boundary representation is periodic boundary conditions which assumes that the system consists of a periodic array (or a crystal ) of identical systems [1], Another common method, developed for the simulation of biomacromolecules, is the stochastic boundary approach, in which the influences of the atoms outside the boundary are replaced by a simple boundary force [78, 79, 80], Warshel uses a Langevin dipoles model in which the solvent is explicitly replaced by a grid of polarizable dipoles. The energy is calculated in a similar way to the polarization energy in a molecular mechanics force field (see above) [15]. 

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]. 

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