About SMoS2:
Structural Motifs of Superfamilies version 2 (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 [1,2,3]. This database currently has 1566 superfamilies with motifs as opposed to the earlier version which had only 110 members [4]. 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.
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 [3].
The motifs belonging to the SMS have been identified by comparing to homologous sequences with thresholds and cutoffs as mentioned in [5]. Further the solvent burial was taken into account to identify motifs. This is the first time this method has been extended to the SMS.
References
- Bhaduri, A., Pugalenthi, G. & Sowdhamini, R.(2004) PASS2: an automated database of protein alignments organised as structural superfamilies . BMC Bioinformatics, 5, 35.
- Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540
- Gandhimathi, A., Nair, A. and Sowdhamini, R. (2011) PASS2.4: An update of database of structure-based sequence alignments of structural domain superfamilies. Nucleic Acids Research. 2011:1-4
- Chakrabarti S, Venkatramanan K, Sowdhamini R.(2003) SMoS: a database of structural motifs of protein superfamilies. Protein Eng.,16(11),791-793.
- Adwait Govind Joshi, Upadhyayula Surya Raghavender and Ramanathan Sowdhamini. (2013) Improved performance of sequence search algorithms in remote homology detection. f1000 Research (in press)
Search Options:
The database may be queried using the superfamily code, superfamily description, PDB code and organism.
- To search by Superfamily code, enter a valid Superfamily code (5-6 digit code as mentioned in SCOP). For example: To search the "globin-like" superfamily, enter "46458" (the SCOP-code)
- To search by superfamily description, enter a valid "superfamily description" (Eg: WRKY DNA-binding domain).
- To search by protein code, enter a valid "PDB ID" (4 digits as mentioned in PDB).
- To search by organism, enter for example: Arabidopsis thaliana.
Previous version of SMoS is found at http://caps.ncbs.res.in/SMoS/
How to cite SMoS2:
NAR Molecular Biology Database Collection entry number 1756 (http://www.oxfordjournals.org/nar/database/summary/1756)
SMoS V2.0 Team:
Dr. Anita Rachel Chacko, Mr. Oommen K. Mathew, Mr. Adwait Joshi, Dr. Upadhyayula Surya Raghavender and Prof. R. Sowdhamini
Contact details:
mini@ncbs.res.in
Lab page:
