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Protein Science, Vol 7, Issue 1 142-149, Copyright © 1998 by Cold Spring Harbor Laboratory Press

ARTICLE

Protein fold recognition without Boltzmann statistics or explicit physical basis

T. HUBER and A. E. TORDA
Research School of Chemistry, Australian National University, Canberra, 0200 Australia

We present a fast method for finding optimal parameters for a low-resolution (threading) force field intended to distinguish correct from incorrect folds for a given protein sequence. In contrast to other methods, the parameterization uses information from >10(7) misfolded structures as well as a set of native sequence-structure pairs. In addition to testing the resulting force field's performance on the protein sequence threading problem, results are shown that characterize the number of parameters necessary for effective structure recognition.
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