An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap

Abstract

The SEAL method has been developed which will optimize the alignment of two three-dimensional structures using their atomic partial charges and steric volumes as factors. In addition, this method will perform the superimposition many times using randomly generated starting configurations and keep only the best unique results based on the value of the alignment function. The computer generated alignments of methotrexate and dihydrofolic acid are compared with the alignments found in the active site of Dihydrofolate Reductase. The marine neurotoxins, saxitoxin and tetrodotoxin, are aligned and the results compared to other alignment techniques. The relationship of the SEAL alignments to the potential field error is explored. Program on disk.