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

ABSTRACT:

Motivation

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.

Result

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

SUBMITTER: Kemena C 

PROVIDER: S-EPMC3232373 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature