Target Submission Instructions
For the experiment to succeed, it is essential that we obtain the help of the experimental community. We invite protein crystallographers, NMR spectroscopists and electron miscroscopy scientists to provide us with information about sequences likely hard for structure modeling (preferably, sequence identity to available structures <50%) that they are working on and can keep on hold for at least 4 weeks after submitting to CASP.
Targets will be released continuously from the beginning of May throughout the end of July, as evenly spaced as possible. Each target will be available for prediction for a period of three weeks, although in some cases we request a longer period to allow it to be used to test refinement and data-assisted methods. It is of course important that there not be any kind of public release of the experimental structure (pictures, abstracts, web-accessible descriptions of the structure, bioRxiv submissions, etc.) until after the predictions for that target are closed.
Just two things to bear in mind. First, because of the timing framework, there should be at least a month between the target submission date and any release of the structure. Second, we ideally need the experimental co-ordinates by the beginning of August and definitely by the end of August, so that the predictions can be assessed. At that point, these can be kept confidential if necessary, though we would like to provide them to those who modeled your structure at the end of November at the latest, so that they can see how well they have done. Participants would also usually like to be able to show slides and discuss their models at the meeting at the beginning of December.
How to submit a target
There are three ways to do that.
Once submitted, we will let you know within 3 days on whether we will use your suggested target for CASP13. In case we take your structure as a CASP13 target, we would ask you to block public access to any structural information about your protein.
PREFERRED: You can submit a target using our Target Submission Form.
If you have not registered with the Prediction Center yet, you would have to do so first. This is a one-time procedure, where you will be asked to provide your contact information.
If you are registered with the Prediction Center, you will have to login and supply only the information about the target.
As alternative to the submission through the Target Submission Form, you can simply send an email to casp AT predictioncenter DOT org containing target's sequence and estimated date of its public release. Information on how the structure was solved (method), protein name, organism name, known ligands, etc. would also be helpful.
Marking PDB deposition as "CASP target" in PDB's submission system.
A special arrangement has been negotiated with the PDB to allow structure depositors to designate their structures as "CASP target" in the PDB's submission system. This way it is possible to submit a structure without any delays. It will not be released until after a certain period of time (currently 8 weeks). In this case there is no need to submit directly to CASP (using options 1 or 2) as in this case we will receive a notification from the PDB.