Protein structure prediction using mutually orthogonal Latin squares and a genetic algorithm.
We combine a new, extremely fast technique to generate a library of low energy structures of an oligopeptide (by using mutually orthogonal Latin squares to sample its conformational space) with a genetic algorithm to predict protein structures. The protein sequence is divided into oligopeptides, and a structure library is generated for each. These libraries are used in a newly defined mutation operator that, together with variation, crossover, and diversity operators, is used in a modified genetic algorithm to make the prediction. Application to five small proteins has yielded near native structures.
Arunachalam
J
J
Department of Crystallography and Biophysics, University of Madras, Chennai 600025, India.
Kanagasabai
V
V
Gautham
N
N
D000465:Algorithms; D000818:Animals; D002645:Chickens; D019295:Computational Biology / Q000379:methods*; D008555:Melitten / Q000737:chemistry / Q000235:genetics; D008840:Microfilament Proteins / Q000737:chemistry / Q000235:genetics; D009842:Oligopeptides / Q000737:chemistry* / Q000235:genetics*; D010191:Pancreatic Polypeptide / Q000737:chemistry / Q000235:genetics; D019151:Peptide Library; D011237:Predictive Value of Tests; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D020598:Proto-Oncogene Proteins c-myb / Q000737:chemistry / Q000235:genetics; D014364:Tryptophan / Q000737:chemistry / Q000235:genetics
D008840:Microfilament Proteins; D009842:Oligopeptides; D019151:Peptide Library; D020598:Proto-Oncogene Proteins c-myb; C026615:villin; D008555:Melitten; C009725:pancreatic polypeptide, avian; D010191:Pancreatic Polypeptide; D014364:Tryptophan