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Briefings in Bioinformatics Advance Access published online on September 26, 2006
Briefings in Bioinformatics, 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
Received March 8, 2006
Accepted August 9, 2006

Original papers

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

Piero Fariselli *, Ivan Rossi, Emidio Capriotti, and Rita Casadio

* To whom correspondence should be addressed.
Piero Fariselli, E-mail: piero{at}biocomp.unibo.it


  Abstract

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.

Piero Fariselli has a PhD in Biophysics and is currently a permanent researcher at the University of Bologna. His main research interests concern structural bioinformatics and machine learning.

Ivan Rossi is the President of BioDec, a Bioinformatic software house, and Adjunct Professor of Computational Biology at the University of Bologna. He has a PhD in Computational Chemistry.

Emidio Capriotti is a Postdoctoral Fellow at the Biocomputing Group. His research concerns different aspects of protein folding related to the prediction of 3D structure, folding kinetics and protein stability.

Rita Casadio is a full Professor of Biochemistry/Bioinformatics and Group Leader of the Biocomputing Group of the Bologna University. Her work is devoted to different problems of computational biology and bioinformatics, including protein structure prediction and sequence analysis.


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