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Bioinformatics 20(Suppl. 1) © Oxford University Press 2004; all rights reserved.

Predicting protein folding pathways

Mohammed J. Zaki 1,*, Vinay Nadimpally 1, Deb Bardhan 1 and Chris Bystroff 2

1 Department of Computer Science and 2 Department of Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA

Received on January 15, 2004; accepted on March 1, 2004

Summary: A structured folding pathway, which is a time ordered sequence of folding events, plays an important role in the protein folding process and hence, in the conformational search. Pathway prediction, thus gives more insight into the folding process and is a valuable guiding tool to search the conformation space. In this paper, we propose a novel ‘unfolding’ approach to predict the folding pathway. We apply graph-based methods on a weighted secondary structure graph of a protein to predict the sequence of unfolding events. When viewed in reverse this yields the folding pathway. We demonstrate the success of our approach on several proteins whose pathway is partially known.

Contact: zaki{at}cs.rpi.edu

* To whom correspondence should be addressed.


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