SMoS : A database of Strucural Motifs of Superfamilies
SMoS database provides information on structural motifs or templates of aligned protein domain superfamilies like PASS2  and CAMPASS  (structural motifs for the CAMPASS database (old-list) will be added soon). Structural motifs are recognized by considering the conservation of amino acid exchange, solvent inaccessibility (primary criteria), secondary structural content, hydrogen bonding, nonpolar interaction and spatial packing of the residues (secondary criteria) among structurally aligned multiple members of protein superfamilies.
The motifs are mapped on the alignment using different color code. Ranking of the motifs is done considering the extent of conservation of the above said criteria amongst superfamily members. Structural motifs can be visualized within the superposed coordinates of the superfamily members by using molecular graphics program like CHIME or RASMOL.
Comparison of the conservation of primary and secondary criteria within the motif and the rest of the protein for each superfamily is represented in graphical format. Spatial orientation of the motifs in terms of distance and angle is provided for each set of motifs. Motifs are also presented in a Dendrogram based on the inter motif spatial distances using PHYLIP . Volume of the motif surrounded space is provided for each superfamily and the depth of motif surrounded region is also mentioned. The sequences of the motif regions are also provided.
Currently, this database contains structural motifs for 110 Multimember Superfamilies of PASS2 database.
Will be available soon
. PASS2: a semi-automated database of protein alignments organised as structural superfamilies. Mallika V, Bhaduri A, Sowdhamini R.. Nucleic Acids Res. 2002 Jan 1;30(1):284-8.
. CAMPASS: a database of structurally aligned protein superfamilies. Sowdhamini R, Burke DF, Huang JF, Mizuguchi K, Nagarajaram HA, Srinivasan N, Steward RE, Blundell TL. Structure. 1998 Sep 15;6(9):1087-94.
. An alternating least squares approach to inferring phylogenies from pairwise distances. Felsenstein, J. Syst Biol. 1997, Mar 46(1), 101-11.
Saikat Chakrabarti : email@example.com
Venkatramanan. K : firstname.lastname@example.org
Sowdhamini. R. : email@example.com