Domain Annotations and Structural Models FAQ

Why should I be interested in the 3D structure of my protein?

Knowledge of a protein's 3D structure can provide critical insights into aspects of its biological function: from catalytic mechanisms and protein–protein interactions to the reasons that specific gene mutations cause harmful disruptions. By combining the annotations from leading structural resources, Genome3D gives a unique perspective on your protein.

Why can't I find protein X?

A given protein may not be found due to the following reasons:

  • It does not belong to the three key model genomes released so far (baker's yeast, ecoli and human)
  • It does not belong to the Uniprot reference proteome set of the corresponding organism
  • It has been added to the Uniprot reference proteome set after Jan 2012 (Uniprot version currently used)

In these cases, it may be best to use Genome3D's  sequence search to find annotations for similar sequences.

Why there are two sections, one for annotations and one for models?

  • Not all resources provide both annotations and models. FUGUE, Gene3d, and pDomThreader provide annotations, DomSerf provides models, and Superfamily and Phyre provide both
  • There is not necessarily 1-to-1 correspondence between models and domains with respect to Superfamily

What other resources provide similar information to Genome3D?


"InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium."


"The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information."

How is Genome3D different to InterPro?

  • InterPro does not contain annotations from PHYRE, pDomTHREADER, FUGUE
  • InterPro does not contain 3D model predictions
  • Genome3D highlights superfamilies that are equivalent between CATH and SCOP
  • Genome3D provides annotations from
  • InterPro calculates a consensus

How should I cite Genome3D?

Please cite the following paper:

 Genome3D: A UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W.A. Buchan, Cyrus Chothia, Alison Cuff, Jose M. Dana, Ioannis Filippis, Julian Gough, Sarah Hunter, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Alex Mitchell, Alexey G. Murzin, Bernardo Ochoa-Montaño, Owen J. L. Rackham, James Smith, Michael J. E. Sternberg, Sameer Velankar, Corin Yeats, and Christine Orengo
Nucleic Acids Res. 2013 January; 41(D1): D499–D507.
Published online 2012 November 30. doi: 10.1093/nar/gks1266