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CAPRI communitywide experiment on the comparative evaluation of protein-protein docking for structure prediction

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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 (on the CAPRI-docking.org, link to page listing the complexes):

  • Protein homo- and hetero-oligomers
  • Protein-peptide complexes
  • Protein-nucleic acid (RNA, DNA) complexes
  • Protein-sugar complexes
  • Protein-Lipid complexes

A CAPRI prediction Round usually takes about 4 weeks. These are preceded by an additional week for participant registration. Ideally therefore, target information should be provided to CAPRI just prior to submitting the publication describing the target structure. Shorter timelines can exceptionally be accommodated as well.

Target information: instructions for authors.

  • Names of the proteins, Uniprot-IDs and some information about their function

  • Provide the amino acid sequences of the constructs used for crystallization of the complex. If applicable, highlight the tags that have been used for purification and not removed before crystallization; indicate if they interfere with the interaction

  • Specify the stoichiometry (or oligomeric state) of the complex, both for homo-oligomers and hetero-oligomers, and indicate if the stoichiometry (oligomeric state) was experimentally determined.

  • If solved but not published yet, provide coordinates of unbound components.

  • 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 Shoshana Wodak), and kept in strict confidence otherwise until permission to release them is granted by the authors.