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- Title
Lattice models of peptide aggregation: Evaluation of conformational search algorithms.
- Authors
Oakley, Mark T.; Garibaldi, Jonathan M.; Hirst, Jonathan D.
- Abstract
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. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1638–1646, 2005
- Subjects
PEPTIDES; PROTEINS; ALGORITHMS; MATHEMATICAL optimization; MONTE Carlo method
- Publication
Journal of Computational Chemistry, 2005, Vol 26, Issue 15, p1638
- ISSN
0192-8651
- Publication type
Article
- DOI
10.1002/jcc.20306