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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.

See: [Tools] [ Secondary Structure Prediction and Domain Assignment ]

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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