Prediction of the folding of short polypeptide segments in proteins by systematic search (original) (raw)

A procedure, CONGEN, for uniformly sampling the conformationd space of short polypeptide segments in proteins has been implemented. Because the time required for this sampling grows exponentially with the number of residues, parameters are introduced to limit the conformationd space that has to be explored. This is done by the use of the empirical energy function of CHARMM (1983) J . Comput. Chem. 4, 187-2171 and truncating the search when conformations of grossly unfavorable energy are sampled. Tests are made to determine control parameters that optimize the search without excluding important configurations. When applied to known protein structures, the resulting procedure is generally capable of generating conformations where the lowest energy conformation matches the known structure within a rms deviation of 1 A.