The GRID Method

It must be relatively easy for anybody working in the field to interpret the output from GRID. 

An annual reappraisal policy was established so that the worst features in the current version of GRID would always be identified, and could be dealt with appropriately in each successive year. 

It is conventional to write impersonally about scientific research, but subjective decisions are made when one decides which features are worst, or which objectives are most important for a program. The personal pronoun we will therefore be used in this article, whenever it is appropriate to draw attention to subjectivity. We are still discussing priorities for the forthcoming release of GRID, but before describing the GRID force field in detail we must first describe how the GRID method actually works. 

There are many programs which can be used compute the electrostatic potential around a molecule. A computer model is first prepared from the x, y, z coordinates of the atoms, and this model is then surrounded by an imaginary orthogonal grid. 

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. 

---

Usually the finite difference method or the grid method is aimed at numerical solution of various problems in mathematical physics. Under such an approach the solution of partial differential equations amounts to solving systems of algebraic equations. 

It is perhaps useful to think of the pattern search method as an attempt to combine the certainty of the multivariate grid method with the ease of the univariate search method, in the sense that it seeks to avoid the enormous numbers of function evaluations inherent in the grid method, without getting involved in the (possibly fruitless and misleading) process of optimizing the variables separately. 

This force field was explicitly intended for use with the GRID method. 

The GRID method differs in three critical ways from traditional programs which just display electrostatic potentials ... 

The GRID method was explicitly designed in order to get selective information about binding sites, and the output can be used in two quite distinct ways ... 

The main advantage of the GRID method is the great variety of available probes, represented by several functional groups such as water, methyl, ammonium, carboxy-late, and benzene in particular, among them there are probes which can both accept and donate a hydrogen bond (e.g. water), probes which cannot turn around (e.g. carbonyl probe), and a recently proposed hydrophobic probe, named DRY. 

Depending on the selected probe and the defined potential energy function, several molecular interaction fields can be calculated. The most common are steric fields and electrostatic fields, sometimes referred as CoMFA fields because originally implemented in CoMFA. Several interaction fields are actually calculated in the - GRID method. 

For the grid method, the number of samples in the composition space is and the number of samples in the noncomposition space is. The grid spacing of the composition variables is =... 

The GRID method, like 3D-QSAR, uses a grid of points at which probe molecules are placed. In this case, however, it is the interaction with the active site of the enzyme rather than with potential drug molecules that is calculated. The most spectacular use of the GRID method was in the discovery of the anti-influenza drug Relenza . 

Jung, K., O. Kwon, H. You (2010). Evaluation of the multivariate accommodation performance of the grid method. Applied Ergonomics 42( 1) 156-161. 

It is worth noting that the system of equations (Eq. 11) is solved numerically by the grid method on the staggered grid [26]. 

---