Calculating and scoring high quality multiple flexible protein structure alignments

This article describes several novel improvements to the Kpax algorithm which allow high quality flexible MSAs to be calculated. This article also introduces a new Gaussian-based MSA quality measure called ‘M-score’, which circumvents the pitfalls of RMSD-based quality measures.
Results: As well as calculating flexible MSAs, the new version of Kpax can also score MSAs from other aligners and from previously aligned reference datasets. Results are presented for a large-scale evaluation of the Homstrad, SABmark and SISY benchmark sets using Kpax and Matt as examples of state-of-the-art flexible aligners and 3DCOMB as an example of a state-of-the-art rigid aligner. These results demonstrate the utility of the M-score as a measure of MSA quality and show that high quality MSAs may be achieved when structural flexibility is properly taken into account.
Availability and Implementation: Kpax 5.0 may be downloaded for academic use at http://kpax.loria.fr/.
Contact: [e-mail]
Supplementary information: Supplementary data are available at Bioinformatics online.

Source: Bioinformatics - August 31, 2016 Category: Bioinformatics Authors: Ritchie, D. W. Tags: STRUCTURAL BIOINFORMATICS Source Type: research