Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome.

ABSTRACT: An ab initio protein structure prediction procedure, TOUCHSTONE, was applied to all 85 small proteins of the Mycoplasma genitalium genome. TOUCHSTONE is based on a Monte Carlo refinement of a lattice model of proteins, which uses threading-based tertiary restraints. Such restraints are derived by extracting consensus contacts and local secondary structure from at least weakly scoring structures that, in some cases, can lack any global similarity to the sequence of interest. Selection of the native fold was done by using the convergence of the simulation from two different conformational search schemes and the lowest energy structure by a knowledge-based atomic-detailed potential. Among the 85 proteins, for 34 proteins with significant threading hits, the template structures were reasonably

SUBMITTER: Kihara D 

PROVIDER: S-EPMC122890 | biostudies-literature | 2002 Apr

REPOSITORIES: biostudies-literature