Pharmacophoric pattern matching in files of three-dimensional chemical structures: characterization and use of...

This paper describes the use of generalized valence angles for the screening of pharmacophoric pattern searches in databases of three-dimensional chemical structures. A generalized valence angle is defined as the angle between two vectors, AB and BC, which have a common vertex B, and in which both vectors correspond to formal chemical bonds; one vector corresponds to a bond and the other to a non-bonded interaction; or both vectors correspond to non-bonded interactions. The screens are identified by a statistical analysis of the frequencies of occurrence of these angle-based features in the Cambridge Structural Database. The occurrence frequencies are discussed and shown to be explicable in terms of small, commonly occurring structural features. The effectiveness of the screens is demonstrated by an extensive series of searches for representative pharmacophoric patterns. The results are compared with those obtained from a similar series of searches using distance-based screens: The latter are found to give a better level of performance, and evidence is presented to suggest that this is due to a high degree of association between the assignments of the angle-based screens.