title: SALIGN: a web server for alignment of multiple protein sequences and structures.
abstract: CONCLUSIONS
  Accurate alignment of protein sequences and/or structures is crucial for many biological analyses, including functional annotation of proteins, classifying protein sequences into families, and comparative protein structure modeling. Described here is a web interface to SALIGN, the versatile protein multiple sequence/structure alignment module of MODELLER. The web server automatically determines the best alignment procedure based on the inputs, while allowing the user to override default parameter values. Multiple alignments are guided by a dendrogram computed from a matrix of all pairwise alignment scores. When aligning sequences to structures, SALIGN uses structural environment information to place gaps optimally. If two multiple sequence alignments of related proteins are input to the server, a profile-profile alignment is performed. All features of the server have been previously optimized for accuracy, especially in the contexts of comparative modeling and identification of interacting protein partners.
  
  
  BACKGROUND
  The SALIGN web server is freely accessible to the academic community at http://salilab.org/salign. SALIGN is a module of the MODELLER software, also freely available to academic users (http://salilab.org/modeller).
  
  
  BACKGROUND
  sali@salilab.org; madhusudhan@bii.a-star.edu.sg.
authors.affiliation: Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.
authors.forename: Hannes
authors.initials: H
authors.lastname: Braberg
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Webb
authors.forename: Elina
authors.initials: E
authors.lastname: Tjioe
authors.forename: Ursula
authors.initials: U
authors.lastname: Pieper
authors.forename: Andrej
authors.initials: A
authors.lastname: Sali
authors.forename: M S
authors.initials: MS
authors.lastname: Madhusudhan
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D020407:Internet; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins