GRID program

The GRID program [Goodford 1985] that is used for finding energetically favourable regions in protein binding sites uses a direction-dependent 6-4 fxmction ... 

Another set of useful 3D-based descriptors for predicting intestinal absorption is through the use of the GRID program. Applications of these descriptors are discussed in Chapter 4. 

The fourth step is dedicated to the identification of the most important interaction areas of map E. This task is carried out using the MINIM utility included into the GRID program. This program collects all points within a certain energy... 

The GRID program [44] has been used by a number of workers as an alternative to the original CoMFA method for calculating interaction fields. An advantage of the GRID approach, apart from the large number of chemical probes... 

In this chapter, I will first describe how MIFs are computed and then give selected examples of how MIFs can be applied. MIFs will be described primarily with reference to their calculation with the GRID program [10]. Other programs may be used to compute MIFs these have different energy functions and parame-trizations. 

The target is also usually considered to have a single titration state and to be unaffected by the position of the probe. However, the GRID program does allow for probe-induced switching between histidine tautomers. 

MIFs are computed for positions of the probe at points on a rectilinear grid superimposed on the target. It is this grid that gives the GRID program its name. 

The empirical energy functions used to compute MIFs can consist of the sum of one or more terms. In the GRID program, the energy function is given by the following terms ... 

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-... 

Davis AM, Gensmantel NP, Johansson E, Marriott DP. The use of the GRID program in the 3-D QSAR analysis of a series of calcium-channel agonists. J Med Chem 1994 37 963-72. 

Some alignment-independent descriptors can be derived from a set of MIFs computed by the GRID program. Pastor et al. developed the GRIND approach (59). Briefly, this method involves two steps ... 

They started from the X-ray structure of thymidylate synthase (from E. coli bacteria) complexed with an inhibitor. A methyl probe was used with the GRID program to produce a contour map of strong interaction with the active site. On the computer screen, a naphthalene molecule (Structure 4.15) was bound into the active site, so that it had maximum overlap with the contours. 

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