Application of structure-based focusing to the estrogen receptor

We present the Cerius(2) Structure-Based Focusing (SBF) application. This application was applied to the estrogen receptor. A series of three-dimensional queries were generated for the binding site of the receptor. The queries consist of combinations of hydrogen bond donors and accepters, and Lipophilic features for the binding site along with excluded volume regions occupied by the receptor atoms. A database of 31 ligands with known relative binding affinities for the estrogen receptor was used to examine the selectivity of the queries. The objective of the study was to determine if queries generated by the Cerius(2) SBF method could differentiate between the more and less active ligands of the training set. Results are promising, with the generated queries showing greater selectivity toward the more active ligands. (C) 2001 John Wiley & Sons, Inc. J Comput Chem 22: 993-1003, 2001.