Molecular surface pattern matching

Whole molecule methods include DOCK and extensions to DOCK allowing ligand flexibility, " " the use of multiconformation databases, 2- molecular surface pattern matching, ellipsoid casting, " AUTODOCK, " " other Monte Carlo and/or simulated annealing methods, - and distance geometry.As already mentioned, excellent reviews of the field of docking are available. 

A similarity assessment of the shapes encoded by these vectors can be carried out on various levels. For two molecules (or conformers) Mj and M2, the number of matches along their C(M ) and C(M2) vectors, divided by the dimension (3 x 861), provides a simple, numerical similarity measure [262]. The comparison of the first 2 x 861 components [i.e., the comparison of vectors C( )(Mi) and C(2)(Mi) to C( )(M2) and C(2)(M2), respectively] appears the most important for a crude shape analysis, since these vectors store the information on the number and type of shape domains occurring for various a and b parameter values. By contrast, a direct comparison of vectors C<3)(M ) and C(3)(M2) gives information on the similarities of the patterns of different shape domains on the two families of molecular surfaces. 

Dean, P.M. and Chau, P.-L. (1987). Molecular Recognition Optimized Searching through Rotational 3-Space for Pattern Matches on Molecular Surfaces. J.MoLGraphics, 5,152-158. 

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