Chemical Matching

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The chemical_matching feature is used to incorporate information about the chemical complementarity of a ligand orientation into the matching process. In this feature, chemical labels are assigned to site points (see Chemical Matching for information on labeling spheres) and ligand atoms (see Ligand File Input/Output) (Kuhl, et al. J. Comput. Chem. 1984). The site point labels are based on the local receptor environment. The ligand atom labels are based on user-adjustable chemical functionality rules. These labeling rules are identified with the chemical_defn_file parameter and reside in an editable file (see chem.defn). A node in a match will produce an unfavorable interaction if the atom and site point components have labels which violate a chemical match rule. The chemical matching rules are identified with the chemical_match_file parameter and reside in an editable file (see chem_match.tbl). If a match will produce unfavorable interactions, then the match is discarded. The speed-up from this technique depends how extensively site points have been labeled and the stringency of the match rules, but an improvement of two-fold or more can be expected.