Lattice models of peptide aggregation: evaluation of conformational search algorithms.
We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems.
Oakley
Mark T
MT
School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom.
Garibaldi
Jonathan M
JM
Hirst
Jonathan D
JD
D000465:Algorithms; D003198:Computer Simulation; D005069:Evaluation Studies as Topic; D008956:Models, Chemical; D009010:Monte Carlo Method; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding
D010446:Peptide Fragments