DIAL

DIAL is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.

This version can accept user-uploaded PDB files.

Where the protein is known to exist as multimers and the transformation matrix is available, the server internally generates multimer coordinates and proposes structural domain solutions for the entire quarternary arrangement.

This version can identify domain boundaries for multiple chain entries and domain swapping events as well.

METHODS

1. Secondary structures are identified on the basis of main chain hydrogen bonding patterns, using the program SSTRUC (Smith, unpublished results), which implements the algorithm of Kabsch and Sander (1983) to define substructures: alpha helix, beta strand and loop regions.

2. C-alpha distances between secondary structures are represented in the form of average values termed "proximity indices".

3. The calculated proximity indices are used to perform clustering using KITSCH, which is a part of the phylogeny inference package PHYLIP and the secondary structural organisation is indicated in the form of dendrograms. Specific nodes in these dendrograms are identified as tertiary structural clusters of the protein; these include supersecondary structures and domains.

4. A ratio of the average proximity indices to the average of all proximity indices, weighted for the aggregation of small subclusters and termed the disjoint factor, is employed as a discriminatory parameter to identify automatically clusters representing individual domains.

REFERENCES

1. R.Sowdhamini & T.L.Blundell (1995).An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Prot. Sci. 4, 506-520.

2. R.Sowdhamini, S.D.Rufino & T.L.Blundell (1996). A database of globular pro tein structural domains: clustering of representative family members into similar folds. Folding and Design, 1, 209-220.

3. Vinayagam, A., Shi, J., Pugalenthi, G., Meenakshi, B., Blundell, T.L. and Sowdhamini, R. (2003) DDBASE2.0: Updated Domain Database with Improved Methods for the Identification of Structural Domains. Bioinformatics 19, 1760-1764 .