Using inferred residue contacts to distinguish between correct and incorrect protein models.

ABSTRACT:

Motivation

The de novo prediction of 3D protein structure is enjoying a period of dramatic improvements. Often, a remaining difficulty is to select the model closest to the true structure from a group of low-energy candidates. To what extent can inter-residue contact predictions from multiple sequence alignments, information which is orthogonal to that used in most structure prediction algorithms, be used to identify those models most similar to the native protein structure?

Results

We present a Bayesian inference procedure to identify residue pairs that are spatially proximal in a protein structure. The method takes as input a multiple sequence alignment, and outputs an accurate posterior probability of proximity for each residue pair. We exploit a recent metagenomic sequen

SUBMITTER: Miller CS 

PROVIDER: S-EPMC2638260 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature