Gibbs sampling and helix-cap motifs.

ABSTRACT: Protein backbones have characteristic secondary structures, including alpha-helices and beta-sheets. Which structure is adopted locally is strongly biased by the local amino acid sequence of the protein. Accurate (probabilistic) mappings from sequence to structure are valuable for both secondary-structure prediction and protein design. For the case of alpha-helix caps, we test whether the information content of the sequence-structure mapping can be self-consistently improved by using a relaxed definition of the structure. We derive helix-cap sequence motifs using database helix assignments for proteins of known structure. These motifs are refined using Gibbs sampling in competition with a null motif. Then Gibbs sampling is repeated, allowing for frameshifts of +/-1 amino acid residue, in o

SUBMITTER: Kruus E 

PROVIDER: S-EPMC1234247 | biostudies-literature | 2005

REPOSITORIES: biostudies-literature