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COVID-19 MODELING RESULTS [2020]

Background

ROUND 2 - 2020 (SARS-2-CoV targets) :: active

Outbreak of the novel coronavirus pandemics (COVID-19) set new challenges for biomedical scientific community. To help understand how the virus spreads and function, the genetic and structrural studies are being carried out all over the world. As of the end of January 2020, the genome of the virus has been decoded. Using the collected sequence data, structural biologists have started working on solving structures of proteins that made up the virus.

CASP has now launched the SARS-2-CoV structure modeling initiative. CASP can make the biggest contribution by generating and evaluating models for the virus' most challenging proteins and domains - those where there is no experimental structure available and where comparative modeling techniques cannot be used. The goal is to obtain the best possible consensus structures, and, critically, to use the family of models to obtain overall and residue level accuracy estimates. The hope is that these structures will be useful to others for gaining further insight into the virus' structure and function, for identifying possible epitopes for vaccine development, and for evaluating possible drug targeting strategies. A number of these proteins form part of complexes, and we anticipate a second phase will be generating models of these assemblies.

An initial analysis of the SARS-2-CoV protein sequences using the CASP target analysis pipeline finds 10 proteins and domains that fit the criteria for template free modeling. We now invite members of the CASP community and others to generate and submit models on these targets.

Subject to feedback from participants, we propose an initial three-week period for model submission, ending April 5th. The model comparison and accuracy analysis will be performed thereafter, in consultation with the appropriate members of the CASP community. Models and analysis will be publicly released as soon as possible.

ROUND 1 - 2018 (NMR nominated targets) :: completed

Together with Dr. Gaetano Montelione (Rutgers), John Tainer (MD Anderson), and Emily Tai (NIH), CASP has launched an initiative to provide structure information for some proteins with high biological significance. For suitable proteins, Dr. Montelione and collaborators will obtain a few experimental structures, usually by NMR. There are three objectives to the program. First, the experimental structures will aid investigators working on these proteins. Second, they will provide a basis for CASP13 targets, both for template free modeling and in some cases also targets for the CASP experiment in data-assisted modeling using sparse NMR and SAXS data. As in CASP12, SAXS data will be provided by Dr. John Tainer's group at the SIBYLS beamline, Advanced Light Source, LNBL. Third, for those proteins where experimental structure determination is not undertaken or unsuccessful, members of the CASP community will be invited to contribute structure models (CASP_Commons). The models will be collated and made available to the investigators requesting the structures, together with estimated accuracy information.

CASP_Commons description

CASP_Commons is a collaborative of members of the CASP community aimed at providing the best possible models to the interested investigators in as useful and convenient a manner as possible.

Note that this endeavor is not part of regular CASP experiments. The suggested targets are proteins where the experimental structure will not be immediately available, and so models cannot be assessed in the traditional CASP way. Rather, the aim is that the models will be of help to the biologists working on these proteins and the process will help build new bridges between the CASP community and the broader community of investigators.

To generate a timely feedback to the biology community, we will start the second round of 'CASP_Commons' immediately. We hope that much of the CASP community would participate, despite the short notice. Registration starts on March 12 (http://predictioncenter.org/casp_commons/registration.cgi). The prediction season starts on March 13, and ends on April 14. The predictors should exercise the usual caution in modeling these targets, checking sequences for signal peptides, disordered regions, and so on. We do not know the oligomerization properties of these proteins, at this time. The CASP_Commons targets will also be re-released in due time as CASP14 targets. Those with structures by October 1, 2020 will be evaluated as regular CASP14 targets.

CASP_Commons is a prototype experiment; if successful we will consider developing it further. We also request feedback and discussion on the best way to manage the process. Please use FORCASP for this purpose. We expect that the CASP_Commons results will be included in the CASP special issue of PROTEINS.

Registration

Participation is open to all.

If you are new to CASP and don't have an account with the Prediction Center, you will have to register with the Prediction Center first and only then proceed to CASP_Commons registration.

If you already have an account with the Prediction Center, you can go directly to the CASP_Commons registration page. Please check, though, that your basic registration information is current. If it has changed - please update it through the My Personal Data link from the main Menu.

Targets

CASP_Commons modeling targets are available on the Target List page.

Model submission

Models can be submitted through the Prediction Submission form available from this web site or by the email provided on the CASP_Commons format page . Please comply with the instructions on submission procedures and format provided there. Please not that in the first round of the experiment we will be accepting only tertiary structure predictions (TS) and estimates of model accuracy (QA, after collecting all TS models).

Results and publication

All CASP_Commons predictions will be made available through this web site. We expect that the CASP_Commons results will be included in the CASP special issue of PROTEINS.
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