Computer methods for molecular design

Abstract
The computational design and simulation of the properties of proteins requires powerful computers, colour graphics and interactive software. A brief description of such a system will be presented. One of the key requirements in the design of novel proteins is the ability to construct a three-dimensional model of the target protein from a knowledge of its amino-acid sequence and the X-ray crystal structure of a homologous protein. Most of the models constructed in this fashion have used the computer as an electronic Dreiding model; where the inserted, deleted, and substituted amino acids are placed in three-dimensional space by subjective, visually oriented procedures (R. J. Read, G. D. Brayer, L. Jurasek & M. N. G. James, Biochemistry 23, 6570 (1984)). An objective computational procedure has been developed whereby the insertions, deletions, and substitutions are performed automatically by making use of a list of rules and a hierarchical energy minimization scheme. The procedure is highly interactive and all of the options are invoked by pointing to the appropriate amino acid residues displayed on the graphics screen. Applications of the procedure and the use of the finished models in enzyme-substrate docking studies for drug design are described.

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