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Predicting the structures of 18 peptides using Geocore

Published online by Cambridge University Press:  01 April 1999

KOHKI ISHIKAWA
Affiliation:
Central Research Laboratories, Ajinomoto Co., 1-1 Suzuki-cho, Kawasaki 210, Japan
KAIZHI YUE
Affiliation:
Department of Pharmaceutical Chemistry, University of California at San Francisco, Box 1204, San Francisco, California 94143
KEN A. DILL
Affiliation:
Department of Pharmaceutical Chemistry, University of California at San Francisco, Box 1204, San Francisco, California 94143
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Abstract

We describe an extensive test of Geocore, an ab initio peptide folding algorithm. We studied 18 short molecules for which there are structures in the Protein Data Bank; chains are up to 31 monomers long. Except for the very shortest peptides, an extremely simple energy function is sufficient to discriminate the true native state from more than 108 lowest energy conformations that are searched explicitly for each peptide. A high incidence of native-like structures is found within the best few hundred conformations generated by Geocore for each amino acid sequence. Predictions improve when the number of discrete φ/ψ choices is increased.

Type
Research Article
Copyright
© 1999 The Protein Society

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