Simultaneous alignment and folding of protein sequences
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Author(s)
Waldispuhl, Jerome
O'Donnell, Charles William
Will, Sebastian
Devadas, Srinivas
Backofen, Rolf
Berger, Bonnie
Date Issued
May 2009
Journal
Research in Computational Molecular Biology
Publisher
Springer Berlin Heidelberg
Citation
Waldispühl, Jérôme et al. “Simultaneous Alignment and Folding of Protein Sequences.” Research in Computational Molecular Biology 2009.
Version
Author's final manuscript
Abstract
Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We presentpartiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm’s complexity is polynomial in time and space. Algorithmically,partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane β-barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments,partiFold-Align significantly outperforms state-of-the-art pairwise sequence alignment tools in the most difficult low sequence homology case and improves secondary structure prediction where current approaches fail. Importantly, partiFold-Align requires no prior training. These general techniques are widely applicable to many more protein families. partiFold-Align is available at http://partiFold.csail.mit.edu.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Massachusetts Institute of Technology. Department of Mathematics
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Attribution-Noncommercial-Share Alike 3.0 Unported
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DOI of Published Version
http://dx.doi.org/10.1007/978-3-642-02008-7_25
