Predicting protein folding pathways

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 conforma...

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Bibliographic Details
Published in:Bioinformatics 2004-08, Vol.20 (suppl-1), p.i386-i393
Main Authors: Zaki, Mohammed J., Nadimpally, Vinay, Bardhan, Deb, Bystroff, Chris
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Computer Simulation
Models, Chemical
Models, Molecular
Molecular Conformation
Protein Conformation
Protein Folding
Proteins - chemistry
Proteins - ultrastructure
Sequence Analysis, Protein - methods
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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.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bth935