Optimization of Site-Directed Mutagenesis. 1. New Random-Centroid Optimization Program for Windows Useful in Research and Development

• Published in: Journal of agricultural and food chemistry Vol. 46; no. 4; pp. 1642 - 1654
• Main Authors: Nakai, Shuryo, Dou, Jinglie, Lo, K. Victor, Scaman, Christine H
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 20.04.1998
• Subjects: algorithms; Biological and medical sciences; Biotechnology; computer software; computer techniques; Fundamental and applied biological sciences. Psychology; Genetic engineering; Genetic technics; mapping; Methods. Procedures. Technologies; optimization; Site specific mutagenesis; site-directed mutagenesis; Computer program; Computer simulation; Algorithm; Optimization; Site directed mutagenesis
• ISSN: 0021-8561; 1520-5118
• DOI: 10.1021/jf970611j

A program of random-centroid optimization was written for Windows 95. The advantages of this new program, over the previous program written in Quick Basic, are easier utilization using a comprehensive step-by-step menu and more efficient and objective mapping. The new program markedly improved the optimization efficiency, as applied to five multimodal functions. Global optimums were found for all functions after 30−40 experiments. Even for the most difficult model, optimization was achieved in ∼50 experiments. A graphical approach enabled by programming in the Windows environment can be a powerful tool for solving nonlinear, multimodal optimization problems, which may be encountered in research and development in chemistry and biology. Keywords: Random-centroid optimization; multimodal optimization; Windows program