CAPRI COVID-19 Updates
We are happy to announce the opening of CAPRI Round 51. This is the first Round of the CAPRI COVID-19 Open Science initiative. Registration to the Round opened Sep 15, 2020 and will end Dec 29, 2020.
A total of 4 targets: T182, T183, T184 and T185, 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 4th target is a multi-component complex of SARS-COV-2 proteins and RNA.
All 4 targets are released once. This Round includes as usual, submissions by servers, human predictors, and a scoring challenge. The timelines will however be longer than for usual CAPRI targets.
Servers will be given ~3 weeks to submit models, human predictors ~10 weeks, and scorers ~4 weeks.
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.
The submitted models can be downloaded at http://cb.iri.univ-lille1.fr/capri/covid.html
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 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 SWISS-MODEL (SWISS-MODEL) 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