An algorithm to parse segment packing in predicted protein contact maps.

ABSTRACT:

Background

The analysis of correlation in alignments generates a matrix of predicted contacts between positions in the structure and while these can arise for many reasons, the simplest explanation is that the pair of residues are in contact in a three-dimensional structure and are affecting each others selection pressure. To analyse these data, A dynamic programming algorithm was developed for parsing secondary structure interactions in predicted contact maps.

Results

The non-local nature of the constraints required an iterated approach (using a "frozen approximation") but with good starting definitions, a single pass was usually sufficient. The method was shown to be effective when applied to the transmembrane class of protein and error tolerant even when the signal become

SUBMITTER: Taylor WR 

PROVIDER: S-EPMC4912788 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature