Characterization of non-trivial neighborhood fold constraints from protein sequences using generalized topohydrophobicity.

ABSTRACT: Prediction of key features of protein structures, such as secondary structure, solvent accessibility and number of contacts between residues, provides useful structural constraints for comparative modeling, fold recognition, ab-initio fold prediction and detection of remote relationships. In this study, we aim at characterizing the number of non-trivial close neighbors, or long-range contacts of a residue, as a function of its "topohydrophobic" index deduced from multiple sequence alignments and of the secondary structure in which it is embedded. The "topohydrophobic" index is calculated using a two-class distribution of amino acids, based on their mean atom depths. From a large set of structural alignments processed from the FSSP database, we selected 1485 structural sub-families includin

SUBMITTER: Fourty G 

PROVIDER: S-EPMC2735972 | biostudies-literature | 2008 Jan

REPOSITORIES: biostudies-literature