Methods
Simulated annealing methods are applied to a simple cubic lattice alpha-carbon model of a 63 amino acid monomeric globular protein. Monomer units occupy only one lattice site and are connected along each lattice edge to their sequence neighbors located in adjacent lattice sites. All conformational changes are required to lie on this lattice. Each simulation begins with a randomly selected, expanded chain with a radius of gyration greater than six times that of comparably-sized folded proteins. At each simulation step the transition to an alternative conformation is selected from a Boltzmann weighted distribution of chain energies for all possible single step transitions accessible to the current chain. Five types of self-avoiding, local moves are available for chain rearrangements, and all allowed moves are found at each simulation step. The energy of each chain is determined from considerations of number and type of nearest- neighbor- non- bonded interactions, chain chirality and radius of gyration. Multiple simulations of greater than 100,000 steps are completed for each randomly chosen starting configuration. The lowest energy forms found in the collapsed states are compared to determine a concensus folding motif. This final configuration has been submitted to the competition.
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