Multiple alignment procedure

Interesting information in this context was also provided by the work of Feher and Schmidt, who proposed two possible alignments between CA4 and other important CSI, including colchicine [33], The represented a test for the newly developed MultiSEAL procedure, which allows the application of the steric and electrostatic alignment (SEAL) [34] method to multiple conformations of multiple molecules. It should be emphasized that, when robust, an alignment method can be profitably used not only to prepare compounds for a 3D-QSAR analysis, but also to identify and locate potential pharmacophoric groups in a set of structurally diverse molecules. The CSI used by Feher and Schmidt were colchicine, CA4, allocolchicine (6), 2-methoxy-5-(2, 3, 4 -trimethoxyphenyl)-tropone (MTC) (7) and 2-methoxyestradiol (8) (Chart 5). 

Database search programs like FASTA [18] or BLAST [19] have been optimised to detect evolutionary relationships between proteins, and are readily adequate for template recognition and (multiple) sequence alignment in cases where the sequence identity is over 25-30% [20], The general procedure is to assume next that the backbone of the model is identical to the one of the template structure and add the side chains onto it [21], although some difficulties may arise with insertions, deletions and local low similarity. 

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