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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