Mutual information and variants for protein domain-domain contact prediction.

ABSTRACT:

Background

Predicting protein contacts solely based on sequence information remains a challenging problem, despite the huge amount of sequence data at our disposal. Mutual Information (MI), an information theory measure, has been extensively employed and modified to identify residues within a protein (intra-protein) that are in contact. More recently MI and its variants have also been used in the prediction of contacts between proteins (inter-protein).

Methods

Here we assess the predictive power of MI and variants for domain-domain contact prediction. We test original MI and these variants, which are called MIp, MIc and ZNMI, on 40 domain-domain test cases containing 10,753 sequences. We also propose and evaluate two new versions of MI that consider triangles of residues and

SUBMITTER: Gomes M 

PROVIDER: S-EPMC3532072 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature