Aladdin software

After ALADDIN, this author and Martin parted ways, but each played a role in the rise of two distinct pharmacophore discovery methods. In 1990, this author joined, as a founding member and first scientist, a new company in Silicon Valley, BioCAD, dedicated to the development of software to assist drug discovery. Our software, Catalyst, contained three components conformational analysis, 3D database searching, and Hypothesis Generation —a novel approach to pharmacophore discovery. Catalyst represented the first fully automated method for pharmacophore discovery. 

Although Catalyst was not a commercial success (the company BioCAD folded in 1994, and the software was taken over by MSI), it stimulated much interest in fully automated pharmacophore discovery. Martin et al. [16] developed DISCO, borrowing code from ALADDIN to detect features and employing a clique detection algorithm mathematically similar to the MNMM method. DISCO also relies on separate, exhaustive conformational analysis, and, in general, produces many pharmacophores consistent with the SAR. 

The basis of ALADDIN is the Daylight Chemical Information Systems software, particularly GENIE, a substructure specification language. When GENIE finds a query substructure in an input SMILES structure, it can return to the user those atoms in the structure that correspond to those hit. Since in a MENTHOR database the coordinates of the atoms are stored in the order in which they occur in the SMILES for that molecule, the coordinates of the atoms of interest are thereby identified. Thus, our geometric objects are established from this set of atoms, and geometric tests are performed on them. Steric tests are performed on molecules that meet the geometric criteria. 

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