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Bioinformatics Advance Access originally published online on October 24, 2006
Bioinformatics 2007 23(1):99-106; doi:10.1093/bioinformatics/btl538
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory

Ruhong Zhou 1,*, Laxmi Parida 1, Kush Kapila 2 and Sudhir Mudur 3

1 Computational Biology Center, IBM T. J. Watson Research Center Yorktown Heights, NY 10598, USA
2 Matrox Imaging Inc., Dorval Quebec, Canada
3 Department of Computer Science, Concordia University Montreal, Canada

*To whom correspondence should be addressed.

Summary: The mechanism of protein folding remains largely a mystery in molecular biology, despite the enormous effort from many groups in the past decades. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates such as the fraction of native contacts, the radius of gyration and so on. In this paper, we present an integrated approach towards understanding the folding process via visual analysis of patterns of these reaction coordinates. The three disparate processes (1) protein folding simulation, (2) pattern elicitation and (3) visualization of patterns, work in tandem. Thus as the protein folds, the changing landscape in the pattern space can be viewed via the visualization tool, PROTERAN, a program we developed for this purpose. We first present an incremental (on-line) trie-based pattern discovery algorithm to elicit the patterns and then describe the terrain metaphor based visualization tool. Using two example small proteins, a ß-hairpin and a designed protein Trp-cage, we next demonstrate that this combined pattern discovery and visualization approach extracts crucial information about protein folding intermediates and mechanism.

Contact: ruhongz{at}us.ibm.com

Supplementary information: http://www.research.ibm.com/people/r/ruhong/SI.htm

Received on August 18, 2006; revised on October 4, 2006; accepted on October 14, 2006

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