S4: structure-based sequence alignments of SCOP superfamilies

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.