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Briefings in Bioinformatics Advance Access originally published online on September 26, 2006
Briefings in Bioinformatics 2007 8(2):78-87; doi:10.1093/bib/bbl032
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© The Author 2006. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

The WWWH of remote homolog detection: The state of the art

Piero Fariselli, Ivan Rossi, Emidio Capriotti and Rita Casadio

Corresponding author. Piero Fariselli, Biocomputing Group, Department of Biology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy. Fax: +39 051 242576; E-mail: piero{at}biocomp.unibo.it

The detection of remote homolog pairs of proteins using computational methods is a pivotal problem in structural bioinformatics, aiming to compute protein folds on the basis of information in the database of known structures. In the last 25 years, several methods have been developed to tackle this problem, based on different approaches including sequence–sequence alignments and/or structure comparison. In this article, we will briefly discuss When, Why, Where and How (WWWH) to perform remote homology search, reviewing some of the most widely adopted computational approaches. The specific aim is highlighting the basic criteria implemented by different research groups and commenting on the status of the art as well as on still-open questions.

Keywords: remote homolog detection, protein structure prediction, sequence alignment, threading, fold recognition

Submitted: March 8, 2006. Received (in revised form): August 9, 2006.


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