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BCL::Fold employs idealized alpha-helices and beta-strands to predict protein structures. A Monte Carlo Metropolis simulated annealing algorithm simulates folding. It optimizes a knowledge-based potential that analyzes radius of gyration, beta-strand pairing, secondary structure element packing, amino acid pair potential, amino acid environment, and loop closure. Discontinuation of the protein chain favors sampling of non-local contacts and thereby creation of complex protein topologies. The algorithm is benchmarked on 66 proteins with lengths between 83 and 293 amino acids. For 61 out of these proteins the best SSE-only models obtained have an RMSD100 below 8.0 Å and recover more than 20% of the native contacts.
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