title: UniAlign: protein structure alignment meets evolution.
abstract: BACKGROUND
  During the evolution, functional sites on the surface of the protein as well as the hydrophobic core maintaining the structural integrity are well-conserved. However, available protein structure alignment methods align protein structures based solely on the 3D geometric similarity, limiting their ability to detect functionally relevant correspondences between the residues of the proteins, especially for distantly related homologous proteins.
  
  
  RESULTS
  In this article, we propose a new protein pairwise structure alignment algorithm (UniAlign) that incorporates additional evolutionary information captured in the form of sequence similarity, sequence profiles and residue conservation. We define a per-residue score (UniScore) as a weighted sum of these and other features and develop an iterative optimization procedure to search for an alignment with the best overall UniScore. Our extensive experiments on CDD, HOMSTRAD and BAliBASE benchmark datasets show that UniAlign outperforms commonly used structure alignment methods. We further demonstrate UniAlign's ability to develop family-specific models to drastically improve the quality of the alignments.
  
  
  METHODS
  UniAlign is available as a web service at: http://sacan.biomed.drexel.edu/unialign
  
  
  BACKGROUND
  ahmet.sacan@drexel.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health System, Drexel University, Philadelphia, PA 19104, USA.
authors.forename: Chunyu
authors.initials: C
authors.lastname: Zhao
authors.affiliation: Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health System, Drexel University, Philadelphia, PA 19104, USA.
authors.forename: Ahmet
authors.initials: A
authors.lastname: Sacan
mesh_terms: D000595:Amino Acid Sequence; D017124:Conserved Sequence; D030562:Databases, Protein; D019143:Evolution, Molecular; D006801:Humans; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins