Predicting protein folding pathways

Authors:
Mohammed J. Zaki;Vinay Nadimpally;Deb Bardhan;Chris Bystroff
Affiliations:
Department of Computer Science;Department of Computer Science;Department of Computer Science;Department of Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
Venue:
Bioinformatics
Year:
2004

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Abstract

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.