Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations.

ABSTRACT: By incorporating predicted secondary and tertiary restraints derived from multiple sequence alignments into ab initio folding simulations, it has been possible to assemble native-like tertiary structures for a test set of 19 nonhomologous proteins ranging from 29 to 100 residues in length and representing all secondary structural classes. Secondary structural restraints are provided by the PHD secondary structure prediction algorithm that incorporates multiple sequence information. Multiple sequence alignments also provide predicted tertiary restraints via a two-step process: First, seed side chain contacts are selected from a correlated mutation analysis, and then an inverse folding algorithm expands these seed contacts. The predicted secondary and tertiary restraints are incorporated int

SUBMITTER: Ortiz AR 

PROVIDER: S-EPMC18658 | biostudies-literature | 1998 Feb

REPOSITORIES: biostudies-literature