(φ,ψ)₂ motifs: a purely conformation-based fine-grained enumeration of protein parts at the two-residue level.

ABSTRACT: A deep understanding of protein structure benefits from the use of a variety of classification strategies that enhance our ability to effectively describe local patterns of conformation. Here, we use a clustering algorithm to analyze 76,533 all-trans segments from protein structures solved at 1.2 Å resolution or better to create a purely φ,ψ-based comprehensive empirical categorization of common conformations adopted by two adjacent φ,ψ pairs (i.e., (φ,ψ)(2) motifs). The clustering algorithm works in an origin-shifted four-dimensional space based on the two φ,ψ pairs to yield a parameter-dependent list of (φ,ψ)(2) motifs, in order of their prominence. The results are remarkably distinct from and complementary to the standard hydrogen-bond-centered view of secondary structure. New insights

SUBMITTER: Hollingsworth SA 

PROVIDER: S-EPMC3268948 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature