Discrete differential geometry of tetrahedrons and encoding of local protein structure (0710.4596v1)

Abstract: Local protein structure analysis is informative to protein structure analysis and has been used successfully in protein structure prediction and others. Proteins have recurring structural features, such as helix caps and beta turns, which often have strong amino acid sequence preferences. And the challenges for local structure analysis have been identification and assignment of such common short structural motifs. This paper proposes a new mathematical framework that can be applied to analysis of the local structure of proteins, where local conformations of protein backbones are described using differential geometry of folded tetrahedron sequences. Using the framework, we could capture the recurring structural features without any structural templates, which makes local structure analysis not only simpler, but also more objective. Programs and examples are available from http://www.genocript.com .