SYBYL 6.9.1/UNITY 4.4.1 software update features the addition of two major scientific technologies, FUGUE and FlexX-Pharm. FUGUE is designed to assist in recognizing distant homologues (divergent evolutionary relationships) by sequence-structure comparison. This program provides structural and functional information about a target sequence and a basis for comparative protein modeling. FlexX-Pharm adds functionality to FlexX, enabling ligand-docking calculations to be guided through interaction (i.e., pharmacophore features) and spatial constraints. This new module provides virtual screening results that conform to a set of optional constraints which can be utilized in the module CScore for ligand selection. This software update also includes code release on multiple platforms.