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 becomes degraded. In the globular class of protein, where the extent of interactions are more limited and more complex, the algorithm still behaved well, classifying most of the important interactions correctly in both a small and a large test case. For the larger protein, this involved examples of the algorithm apportioning parts of a single large secondary structure element between two different interactions. Conclusions: It is expected that the method will be useful as a pre-processor to coarse-grained modelling methods to extend the range of protein tertiary structure prediction to larger proteins or to data that is currently too 'noisy' to be used by current residue-based methods.