Combining co-evolution and secondary structure prediction to improve fragment library generation

Abstract Motivation Recent advances in co-evolution techniques have made possible the accurate prediction of protein structures in the absence of a template. Here, we provide a general approach that further utilizes co-evolution constraints to generate better fragment libraries for fragment-based protein structure prediction. Results We have compared five different fragment library generation programmes on three different datasets encompassing over 400 unique protein folds. We show that considering the secondary structure of the fragments when assembling these libraries provides a critical way to assess their usefulness to structure prediction. We then use co-evolution constraints to improve the fragment libraries by enriching them with fragments that satisfy constraints and discarding those that do not. These improved libraries have better precision and lead to consistently better modelling results. Availability and implementation Data is available for download from: http://opig.stats.ox.ac.uk/resources. Flib-Coevo is available for download from: https://github.com/sauloho/Flib-Coevo. Supplementary information Supplementary data are available at Bioinformatics online.