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Nucleic Acids Research Advance Access originally published online on May 13, 2008
Nucleic Acids Research 2008 36(Web Server issue):W246-W251; doi:10.1093/nar/gkn259
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W246-W251
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

pFlexAna: detecting conformational changes in remotely related proteins

Anshul Nigham1,2, Lisa Tucker-Kellogg1,2, Ivana Mihalek3, Chandra Verma3 and David Hsu1,4,*

1Department of Computer Science, National University of Singapore, Singapore 117590, 2Singapore–MIT Alliance, Singapore 117576, 3Bioinformatics Institute (A*STAR), Singapore 138671 and 4Graduate School of Integrative Sciences & Engineering, National University of Singapore, Singapore 117456

*To whom correspondence should be addressed. Tel: +65 6516 2978; Fax: +65 6779 4580; Email: dyhsu{at}comp.nus.edu.sg

Received February 21, 2008. Revised April 11, 2008. Accepted April 20, 2008.

The pFlexAna (protein flexibility analyzer) web server detects and displays conformational changes in remotely related proteins, without relying on sequence homology. To do so, it first applies a reliable statistical test to align core protein fragments that are structurally similar and then clusters these aligned fragment pairs into ‘super-alignments’, according to the similarity of geometric transformations that align them. The result is that the dominant conformational changes occur between the clusters, while the smaller conformational changes occur within a cluster. pFlexAna is available at http://bigbird.comp.nus.edu.sg/pfa2/.


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