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The DomFOLD Protein Domain Boundary Prediction Server

About the server

The DomFOLD Protein Domain Prediction Server allows you to predict the number of domains and their possible boundaries within a protein sequence. Two methods are available: DomFOLD and DomFOLDpdp. In the DomFOLD method, the output from DomSSEA, DISOPRED and HHsearch is parsed to form a consensus domain prediction (Figure 1). In the DomFOLDpdp method, the top fold recognition model from nFOLD3 is analysed using the program PDP (Figure 2).


Figure 1 DomFOLD prediction for the hard 2 domain CASP8 target T0462. The native structure has been coloured in accordance with the domain boundary predicted by DomFOLD during the CASP8 experiment. The image was rendered using Pymol.


Figure 2 DomFOLDpdp prediction for the 5 domain CASP8 target T0487. The native structure has been coloured in accordance with the domain boundaries predicted by DomFOLDpdp. The image was rendered using Pymol. N.B. DomFOLDpdp is a new method and did not participate in CASP8, however the nFOLD3 model used by DomFOLDpdp was a blind prediction.

DomFOLD Submission Form

News

  • The latest DomFOLD method is now integrated with the IntFOLD server.
  • September 2008: Version 2.0 of the server is now online, which includes the new DomFOLDpdp method.
  • March 2008: The new DomFOLD server will be available in time for CASP8.

References

The DomFOLD method incorporates the following methods: DomSSEA, DISOPRED and HHsearch

  • Marsden, R., McGuffin, L. J. & Jones, D. T. (2002) Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Science, 11, 2814-2824.  PubMed
  • Ward, J. J., Sodhi, J. S. McGuffin, L. J., Buxton, B. F. & Jones, D. T. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol., 337, 635-645. PubMed
  • Söding J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics. 21, 951-96. PubMed

The DomFOLDpdp method uses the PDP program:

  • Alexandrov, N. & Shindyalov, I. (2003) PDP: protein domain parser. Bioinformatics. 19, 429-30. PubMed

Contact

Tel: 0118 378 6332

Email: l.j.mcguffin
@reading.ac.uk

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