SSToSS : A database of Sequence Structural Templates of Singlemember Superfamilies

 

Description :

SSToSS is a database which provides sequence-structural templates of single member protein domain superfamilies like PASS2 [1]. Sequence-structural templates are recognized by considering the content and overlap of sequence similarity and structural parameters like, solvent inaccessibility, secondary structural content, hydrogen bonding and spatial packing of the residues among the protein of single member superfamilies.

The templates are mapped on the sequence using different color code. Sequence-structural templates can be visualized within the three dimensional structure of the superfamily member by using molecular graphics program like CHIME or RASMOL Spatial orientation of the templates in terms of distance and angle is provided for each set of templates. Templates are also presented in a Dendrogram based on the inter motif spatial distances using PHYLIP [2]. The sequences of the sequence-structural motif regions are also provided.In the SSToSS database we incorporated related sequence search option [3] based on multiple-pattern matching combined with a search for statistically significant sequence similarity. The specificity of the search engine is increased by utilizing the inter-motif spacing and pair wise global alignment of the query and hits.

SSToSS database also utilizes an alignment algorithm [4] to provide multiple alignment of the similar sequences identified by multiple-motif based database search. It allows the user to obtain a control over the alignment by providing sequence-structure template regions as input to the alignment program to achieve a more structurally relevant and functionally useful alignment of protein sequences. The algorithm employs local conserved regions of the sequences to be fixed and aligns the rest based on normal progressive alignment. The chances of global misalignment are thereby reduced and the possibility of obtaining overall better alignment is increased [4].

We also provide three dimensional model structures of the similar sequences identified by multiple-motif based similarity search as potential member of each SSToSS superfamily. 3D models are built using the program MODELLER [5] based on the structure of superfamily member protein

Currently, this database contains structural motifs for 613 single member superfamilies of PASS2 database.

List of superfamilies

More information

Download Rasmol and Chime

References:

[1]. PASS2: a semi-automated database of protein alignments organised as structural superfamilies. Mallika V, Bhaduri A, Sowdhamini R. Nucleic Acids Res. 2002, 30, 284-8.

[2]. An alternating least squares approach to inferring phylogenies from pairwise distances. Felsenstein, J. Syst Biol. 1997, 46, 101-11.

[3]. SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs. Chakrabarti, S., Anand, A.P, Bhardwaj, N., Pugalenthi, G. and Sowdhamini, R. Nucleic Acids Res. 2005, 33, W274-W276.

[4]. Improvement of alignment accuracy utilizing sequentially conserved motifs. Chakrabarti, S., Bhardwaj, N., Anand, P.A. and Sowdhamini, R. BMC Bioinformatics. 2004, 5, 167-179.

[5]. Comparative protein modelling by satisfaction of spatial restraints. Sali, A. and Blundell, T.L. J Mol Biol. 1993, 234, 779-815.

 


Contact Adressess:

Sowdhamini. R. : mini@ncbs.res.in

Saikat Chakrabarti : saikat@ncbs.res.in

Pugalenthi.G : pugal@ncbs.res.in