SWISS-MODEL WORKSPACE TUTORIAL
2. My protein is quite large, and would like to identify individual domains I could model separately.
Many proteins are modular
and made up of several structurally distinct domains, which often
reflect evolutionary relationships and may correspond to units of
molecular function.The sensitivity and performance of profile-based
template search methods can often be improved when the template search
is performed on individual domains rather than the whole target sequence.
The member databases
of InterPro (Mulder
et al.) allow for both the identification of protein domains
and the assignment of protein function. Using the InterPro Domain
Scan (IprScan, Zdobnov
et al.), protein domains and functional sites can be assigned
to regions of a target sequence.
Let's use the example of Collagen alpha 3(VI) chain (UniProt accession code: P12111) to identify individual domains in the target sequence. The result looks like this:
The location of the individual domains is provided in tabular form below the graphics. Links to the motif definition in InterPro are provided.
Interpro Scan has finished. Here are the results: IPR002035: von Willebrand factor, type A, Domain PF00092: 39 - 213 VWA PF00092: 242 - 415 VWA PF00092: 445 - 620 VWA PF00092: 639 - 812 VWA PF00092: 837 - 1009 VWA PF00092: 1029 - 1201 VWA PF00092: 1233 - 1404 VWA PF00092: 1436 - 1609 VWA PF00092: 1639 - 1812 VWA PF00092: 2402 - 2581 VWA PF00092: 2619 - 2810 VWA
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