@Article{Waldispuhl_ODonnell_Will-Simul_Align_and-JCB2014,
  author =	 {Waldispuhl, Jerome 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}},
  journal =	 JCB,
  year =	 {2014},
  volume =	 {21},
  number =	 {7},
  pages =	 {477-491},
  user =	 {backofen},
  pmid =	 {24766258},
  doi = 	 {10.1089/cmb.2013.0163},
  issn = 	 {1066-5277},
  issn = 	 {1557-8666},
  abstract =	 {Abstract Accurate comparative analysis tools for 
                  low-homology proteins remains a difficult challenge in 
                  computational biology, especially sequence alignment and 
                  consensus folding problems. 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 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 
                  beta-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 and multiple sequence alignment tools in the most 
                  difficult low-sequence homology case. It also 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/ ).}
}