Fold prediction of helical proteins using torsion angle dynamics and predicted restraints.

ABSTRACT: We describe a procedure for predicting the tertiary folds of alpha-helical proteins from their primary sequences. The central component of the procedure is a method for predicting interhelical contacts that is based on a helix-packing model. Instead of predicting the individual contacts, our method attempts to identify the entire patch of contacts that involve residues regularly spaced in the sequences. We use this component to glue together two powerful existing methods: a secondary structure prediction program, whose output serves as the input to the contact prediction algorithm, and the tortion angle dynamics program, which uses the predicted tertiary contacts and secondary structural states to assemble three-dimensional structures. In the final step, the procedure uses the initial set

SUBMITTER: Zhang C 

PROVIDER: S-EPMC122566 | biostudies-literature | 2002 Mar

REPOSITORIES: biostudies-literature