Prediction of peptide conformation using a scale-transformed entropy sampling algorithm.
An algorithm for predicting the lowest energy structure of a peptide has been developed. High-energy barriers on an energy surface can be easily overcome by logarithmically transforming the energy space. For efficient optimizations, the energy space is searched using a scale-transformed entropy sampling method, and conformations specific to a primary structure of the peptide are sampled with large weights. The efficiency of the present method is demonstrated by calculations on cholecystokinin octapeptide (CCK-8).
Nakamura
Hideaki
H
Department o Functional Materials Engineering, Fukuoka Institute of Technology, Japan. h-naka@fit.ac.jp
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D019277:Entropy; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D012844:Sincalide / Q000737:chemistry; D013816:Thermodynamics
D010455:Peptides; D012844:Sincalide