title: S4: structure-based sequence alignments of SCOP superfamilies.
abstract: S4 is an automatically generated database of multiple structure-based sequence alignments of protein superfamilies in the SCOP database. All structural domains that do not share more than 40% sequence identity as defined by the ASTRAL compendium of protein structures are included. The alignments are constructed using pairwise structural alignments to generate residue equivalences that are then integrated into multiple alignments using sequence alignment tools. We describe the database and give examples showing how the automatically generated S4 alignments compare favourably to hand-crafted alignments. Available at: http://compbio.mds.qmw.ac.uk/S4.html.
authors.affiliation: Institute for Cell and Molecular Science, Bart's and The London, Queen Mary's School of Medicine and Dentistry, University of London, 32 Newark Street, London E1 2AA, UK.
authors.forename: James
authors.initials: J
authors.lastname: Casbon
authors.forename: Mansoor A S
authors.initials: MA
authors.lastname: Saqi
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000145:classification*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins