STRIKE: evaluation of protein MSAs using a single 3D structure

Bioinformatics
Carsten KemenaCedric Notredame

Abstract

Evaluating alternative multiple protein sequence alignments is an important unsolved problem in Biology. The most accurate way of doing this is to use structural information. Unfortunately, most methods require at least two structures to be embedded in the alignment, a condition rarely met when dealing with standard datasets. We developed STRIKE, a method that determines the relative accuracy of two alternative alignments of the same sequences using a single structure. We validated our methodology on three commonly used reference datasets (BAliBASE, Homestrad and Prefab). Given two alignments, STRIKE manages to identify the most accurate one in 70% of the cases on average. This figure increases to 79% when considering very challenging datasets like the RV11 category of BAliBASE. This discrimination capacity is significantly higher than that reported for other metrics such as Contact Accepted mutation or Blosum. We show that this increased performance results both from a refined definition of the contacts and from the use of an improved contact substitution score. cedric.notredame@crg.eu STRIKE is an open source freeware available from www.tcoffee.org Supplementary data are available at Bioinformatics online.

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Citations

Jul 4, 2017·Genomics·Biswanath Chowdhury, Gautam Garai
May 26, 2017·Bioinformatics·Cristian Zambrano-VegaJosé F Aldana-Montes
Nov 29, 2015·Briefings in Bioinformatics·Maria ChatzouCedric Notredame
Jan 1, 2020·BMC Bioinformatics·Emanuel Maldonado, Agostinho Antunes

Datasets Mentioned

BETA
U117581331

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