@inproceedings{Waldispuehl:etal:TMBalign:RECOMB09,
author = {Waldispühl, Jérôme and 
          O'Donnell, Charles W. and Will, Sebastian and  Devadas, Srinivas
          and Backofen, Rolf and Berger, Bonnie},
title = {Simultaneous Alignment and Folding of Protein
         Sequences},
booktitle = {RECOMB09},
year = {2009},
doi = {10.1089/cmb.2013.0163},
volume = {5541},
user = {will},
series = {LNBI},
publisher = {Springer},
pages = {339--355},
location = {Heidelberg},
isbn = {978-3-642-02007-0},
editor = {Serafim Batzoglou},
abstract = {One of the central challenges in computational
            biology is to develop accurate tools for protein
            structure analysis. Particularly difficult cases of
            this are sequence alignment and consensus folding of
            low-homology proteins. In this work, we present
            partiFold-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 additionally
            exploits sparsity in the set of likely
            super-secondary structure pairings and alignment
            candidates for each amino acid to achieve an
            effectively cubic running time for simultaneous
            pairwise alignment and folding. We demonstrate the
            efficacy of these techniques on transmembrane
            beta-barrel proteins, an important yet difficult
            class of proteins with very few available
            three-dimensional structures. In tests on sequence
            alignments derived from structure alignments,
            partiFold-Align is significantly more accurate than
            current best approaches for pairwise sequence
            alignment in the difficult case of low sequence
            homology and improves secondary structure prediction
            when current approaches fail. Importantly,
            partiFold-Align does not require training on
            transmembrane beta-barrel proteins. The generality
            of these techniques should allow them to be applied
            to a wide variety of protein structures.}
}