This page provides you information about how a CAPRI prediction round is organised and how to contribute targets to CAPRI.
Table of contents
The organisation of a CAPRI prediction round
CAPRI heavily relies on the willingness of structural biologists to offer the coordinates of complexes they just determined but didn’t publish yet, as targets for a CAPRI experiment (Round).
Complexes that qualify as targets for CAPRI must be structures (determined using x-ray crystallography, NMR or high resolution Cryo-EM) that have not yet been published or publicly described in the literature or the Internet. They must be complexes (dimers of higher order assemblies) where the protein moiety is bound to another protein, to an oligo peptide, to nucleic acids (DNA or RNA), oligosaccharides or lipids. Protein assemblies comprising identical subunits (homo-oligomers) also qualify.
A CAPRI prediction Round is initiated each time a target (or a few targets) become available, and completed three to six weeks later. Offering your complex as a target for CAPRI should not delay publication, provided the target is offered just before the paper describing it is submitted. You may also be assured that target information is kept strictly confidential until specified otherwise by you, the author.
Over 50 structural biologists worldwide have offered targets to CAPRI in the past, with some doing so repeatedly (see our contributors). They have been personally acknowledged and cited in all CAPRI publications describing prediction results. More than once these results have also contributed new insights into the biological function of the corresponding complexes. We very much hope therefore, that you will join their rank in the future.
Practical aspects: How to contribute a target?
CAPRI target information and any related inquiries should be sent to: targets_[at]_capri-docking.org
General information:
CAPRI is interested in targets representing a wide range of complexes:
- Protein homo- and hetero-oligomers
- Protein-peptide complexes
- Protein-nucleic acid (RNA, DNA) complexes
- Protein-glycan complexes
- Protein-lipid complexes
A CAPRI prediction Round is initiated each time a target (or several targets) become available, and is completed three to six weeks later. The window for offering your complex as a target for CAPRI goes from the moment of data collection to just before the preprint and/or paper describing it is submitted, such that the prediction window closes by the time the publication (or preprint if applicable) becomes available In the current digital era, we encourage early submission in order t oavoid images of the complex appearing on-line. For high-profile targets however, we can accommodate shorter timelines.
Target information: instructions for authors.
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Names of the proteins (or other biomolecules), Uniprot-IDs and some information about their function
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Amino acid sequences of the constructs used for the experimental characterisation of the complex
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If dealing with nucleic acids or other molecules (e.g. glycans), their sequence (and connectivity if relevant)
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The stoichiometry of the complex, both for homo-oligomers and hetero-oligomers, and indicate if it has been experimentally determined.
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If possible, provide the unpublished atomic coordinates of the target complex, in PDB format. These coordinates will be used only by the CAPRI assessment team (Marc Lensink, and Alexandre Bonvin) and kept in strict confidence otherwise until permission to release them is granted by the authors. Importantly, these do not need to be available at the time of target provision, but will be required for later assessment of the predictions.