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.
Contact Adressess: Sowdhamini. R. : mini@ncbs.res.in Saikat Chakrabarti :
saikat@ncbs.res.in Pugalenthi.G :
pugal@ncbs.res.in
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.