Information Page

 

This version of SMoS database contains structural motifs for the multimember superfamilies of PASS2 database. Structural motifs are identified considering the conservation of the following criteria

Primary criteria:

Secondary criteria:

 

Motifs are marked on the alignment using different color codes. Same color code is maintained in the dendrogram and in the spatial representation of the motifs in superposed 3 dimensional coordinates.

Comparison of primary and secondary criteria between the motif and the rest of the protein are represented in graphical format within graph section.

For each set of motifs three dimensional orientation is represented in terms of spatial distances. Distances and absolute angle of each motifs with respect to the centre of mass of the protein are calculated and average values for the superfamily members are presented in a tabular format in spatial orientation section. Inter motif distances and torsional angles are also calculated and presented in a matrix format.

The average volume of the motif surrounded region is calculated and the percentage fraction of the same with respect to the average volume of the proteins in the superfamily is also provided.

The total percentage length of the motifs with respect to the whole alignment length is provided. The depth of the motif surrounded space from the surface of the whole protein is calculated. An average value of depth for each set of motifs is also provided.