SMoS2 database provides the most recent update of information on structural motifs of aligned protein domain superfamilies in PASS2 which is in direct correspondence with SCOP 1.75. This database currently has 1566 superfamilies with motifs as opposed to the earlier version which had only 110 members. They have been segregated into three main groups namely the SMS (single membered superfamilies), TMS (two membered superfamilies) and MMS (multi-membered superfamilies). Each of these are sub divided into the seven classes based on the SCOP classification. Motifs have been mapped for visualization on to an alignment as well as the structure. The motifs are mapped on the alignment using different color codes. 3-D visualization of the motifs has been provided using JMOL.

     Structural motifs are recognized by considering the conservation of amino acid exchange, solvent inaccessibility (primary criteria), secondary structural content, hydrogen bonding, non-polar interaction and spatial packing of the residues (secondary criteria) among structurally aligned multiple members of protein superfamilies taken from PASS2.

     The motifs belonging to the SMS have been identified by comparing to homologous sequences with thresholds and cutoffs as mentioned in. Further the solvent burial was taken into account to identify motifs. This is the first time this method has been extended to the SMS.

SMoS V2.0 Team

Dr. Anita Rachel Chacko,
Mr. Oommen K. Mathew,
Mr. Adwait Joshi,
Dr. Upadhyayula Surya Raghavender
and Prof. R. Sowdhamini