CAPRI: Critical Assessment of PRediction of Interactions

Registration to Round 51 opened Sep 15, 2020 and will end Dec 29, 2020.A total of 4 targets are being offered in this Round. Three are complexes of SARS-COV-2 proteins with human host proteins (prioritized from the interaction proteomics study of Gordon et al. (2020) [1]) and the 4^th target is a multi-component complex of SARS-COV-2 proteins and RNA. Description of the Round can be found at: https://www.ebi.ac.uk/pdbe/complex-pred/capri/covid-capri/

Round 51 will be conducted in the spirit of open science. Models submitted by all groups/teams will be made immediately available online after the submission deadline in full transparency. Since for many of the considered targets, experimental structures may not be available for some time to evaluate predicted models, participating groups will work together to evaluate the quality of submitted models, compare and rank them on the basis of agreed-upon criteria and derive consensus predictions whenever appropriate. The protocol for this evaluation will be worked out after the Round is completed.  We remind everyone that the plan is to report the results of this collective effort in a common publication coauthored by members of all participating groups/teams.

1. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing,

Gordon DE et al., Nature. 2020 Jul;583(7816):459-468. doi: 10.1038/s41586-020-2286-9. Epub 2020 Apr 30.

The CASP14 season will open May 18 and run until approximately July 30, 2020. The first assembly target will be offered during the week of May 25.  Members of both the CASP and CAPRI communities will be invited to model the interfaces of protein hetero-complexes, homo-multimers and domain-domain interactions in CASP14 assembly targets. Description of the CASP14 experiment can be found at: http://predictioncenter.org/casp14/index.cgi

CAPRI participants wishing to take part in Round 50 are invited to register for the entire round in advance.  Registration is now open. As in previous joint experiments we require CAPRI participants to register also with the CASP14 season. Only groups registered with both experiments will be part of the joint CASP-CAPRI experiment (for further details please consult the CASP-CAPRI page using the link on the top menu).

 The CAPRI community is mobilizing its resources and expertise to model the 3D structures and interaction interfaces of SARS-COV-2 - human protein complexes and larger assemblies (homo- or hetero-complexes) starting from experimentally determined structures (by x-ray diffraction or cryo-EM), or from predicted structure, of the individual components.

An important focus of our initiative is to prioritize relevant COVID-19 complexes that will be offered as target for community-wide CAPRI prediction Rounds. These prediction Rounds will be run as a collaborative undertaking where data, analyses and results will be closely integrated and widely shared, hopefully moving COVID-19 science fast forward.

Whenever possible our initiative will leverage COVID-19 efforts of CASP (CASPcommons) ) and the SIB/Modeller (SIB/MOdeller) on predicting the 3D structure of individual proteins, by using the high-quality models they produce to predict the association modes of these proteins.

 The CAPRI community remains eager to continue to improve and test their modeling tools by taking on increasingly challenging prediction problems.  In the spirit of open science we hence call upon structural biologists working on COVID-19 related protein complexes to offer these complexes as targets for CAPRI prediction Rounds prior to publication (for details how this is done see contributing targets.) 

If you are interested in joining our initiative or exploring a collaboration, please contact us at: capri.docking@gmail.com

Target 163 is an interesting, and likely challenging prediction problem. The target is a heterocomplex with A2B2 stoichiometry (confirmed experimentally) of two small helical protein components of the synaptonemal complex.

We are happy to announce CAPRI Round 48, with Targets T161 and T162. The systems of both targets is a toxin-antitoxin complex.

Predictors and scorers are requested to register for the entire Round.

Additional notes:

We are announcing the first round of 2019, Round 47. Please see Round 47 page for registration and more details.

This round features one target, Target 160. The is the assembly domain of SAP the surface layer (S-layer) protein from a highly pathogenic microbe. This assembly domain comprises 6 discrete structural domains, which self assemble into a 2D array whose structure is currently under study by Cryo-EM.

Protein-protein interactions and other interactions between macromolecules are essential to all aspects of biology and medical sciences, and a number of methods have been developed to predict them. CAPRI is a community wide experiment designed to assess those that are based on structure. If we know the 3D structure of two components of a complex and build a model of their assembly, how reliable and accurate is that model likely to be?

CAPRI is a blind prediction experiment managed by Capri management. Its targets are unpublished crystal or NMR structures of complexes, communicated on a confidential basis by their authors to the CAPRI management. Participant predictor groups are given the atomic coordinates of two proteins that make biologically relevant interactions. They model the target complex with the help of the coordinates and other publicly available data (sequence, mutations etc~), and submit sets of ten models for assessment on the CAPRI Web site. In addition, the predictors are invited to upload larger sets that are communicated to scorer groups who evaluate and rank them, and make a separate ten-model submission. After the prediction round is completed, the CAPRI assessors compare the submissions to the experimental structure, et evaluate the models on criteria that depend on the geometry and biological relevance of the predicted interactions.

Since CAPRI began in 2001, the experiment has had two to four prediction rounds each year, with one or a few targets per round. Each round is announced a week in advance, it lasts 3-6 weeks, and the results are known in the following weeks. To be on the mailing list, please send a message to Sameer Velankar.

Structural biologists and scientists actively engaged in the study macromolecular interactions are invited to participate: 

• by offering targets - more information 
• by registering prediction rounds as predictors and/or scorers 

Please read and observe the rules of the experiment and the confidentiality agreement that all CAPRI participants must sign.

Information on targets of past CAPRI rounds is available here.