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![[Figure 2]](ba0010fig2mag.jpg)
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Figure 2
Domain database (DDBASE) WWW page for the B chain of abrin (PDB code, 1abr) as an example. Domains have been identified using the program DIAL (Sowdhamini & Blundell, 1995  ). The organization of structural domains can be viewed as secondary structural dendrograms where helices and extended strands have been clustered on the basis of intersecondary structural inter-Cα distances. Various combinations of nodes, corresponding to secondary-structural clusters, have been examined for structural compactness and listed along with their disjoint factor (see Sowdhamini & Blundell, 1995, for details). Domain boundaries for all these possibilities can be accessed by clicking on that entry. Further, detailed outputs can be accessed for the `best' combination. The `best' combination is usually the one with the highest disjoint factor (Df) without any secondary structures being ignored (-Nst. column shows the number of secondary structures that are ignored while examining various nodes in the dendrogram). The protein chain can be viewed using RASMOL (Sayle & Milner-White, 1995) where domains are coloured differently in the case of multi-domain proteins. |
![[Figure 2]](ba0010fig2.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
