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S4: Structure-based Sequence Alignments of SCOP Superfamilies (RRID:SCR_007911)Copy Citation Copied
URL: http://compbio.mds.qmw.ac.uk/~james/S4.shtml
Proper Citation: S4: Structure-based Sequence Alignments of SCOP Superfamilies (RRID:SCR_007911)
Description: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The S4 database contains sequence alignments of domains in SCOP superfamilies. The aligned domains are selected using ASTRAL so that no two domains in the alignment have more than 40 percent identity and, moreover, they align all domains identified by ASTRAL as having less than 40 percent sequence identity. The alignments are generated using information from pairwise structural alignments of all domains in a given superfamily. These structural alignments generate residue equivalences and distances between residues, as well as an overall similarity of the two domains being compared (RMSD). This information is used to score individual the equivalences between residues. The scores are then integrated using a multiple sequence alignment program to generate the finished alignment. This database allows alignments to be retrieved in clustal format, or viewed in a web browser, with either structural or sequence features annotated. In addition, the statistics of structural diversity for each superfamily can be seen. The pairwise structural alignments were performed using the SAP program. The output of SAP was converted to a T-Coffee library so that the multiple sequence alignment T-Coffee could be use to compute the sequence alignments.
Synonyms: S4
Resource Type: data or information resource, database
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