Molecular Docking Prediction of Biomacromolecular Binding

There are nmnerous cases of proteins for which structures have been determined in more than one state of ligation. In some cases, the structures undergo little change, except perhaps for specific and localized changes associated with particular fimctional residues. 

TABLE 9.4 Some tools (programs) for molecular docking 

This program combines a GA and a local gradient minimization with CHARMM as the scoring function for flexible docking of protein complexes. The populations ate modified by standard mutation and crossover operators. 

Flexible Ligand Oriented on a Grid selects ligands from a DB, complementary to a receptor of known 3D structure. Distances between favorable sites of interaction in the protein are calculated along with atomic distances of the ligand. The ligand is then superimposed onto the protein interaction sites, optimized and scored with a function that includes van der Waals, electrostatic, HB and /1. 

A high correlation score denotes good surface complementarity between the molecules. 

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