16th Community Wide Experiment on the
Critical Assessment of Techniques for Protein Structure Prediction

Prediction Center
Questions and Answers

I have determined a structure of a protein/RNA and want to suggest it as a prediction target for CASP16. How can I do that?
There are three easy ways to suggest your protein/RNA for CASP. You can either directly submit the sequence of your macromolecule and the related information through the web form; mark your PDB deposition as 'CASP target' (check box) within the PDB deposition system; or send us an email (casp AT predictioncenter.org).

I am not in structure determination business, but want to model a protein/RNA of my interest. Can I submit the sequence of this protein/RNA as a CASP target, so that the CASP community will model it for me?
No, CASP is not a structure modeling facility but rather a forum for objective testing structure prediction methods. However, we have good news for you. If you want to model a protein or protein complex, model(s) can be already available in the AlphaFold Protein Structure Database. Also, there are several protein structure prediction servers, which were tested in CASP and proved to be reliable structure prediction tools. They can compute the structure of your protein together with the accuracy estimates of the generated models. In particular, you can use: ColabFold notebook (based on AlphaFold2 and MMseqs2) or RosettaFold server.

Where can I find the list of CASP16 targets?
Targets suggested for prediction in CASP16 can be found at the Target List page . During the prediction season, targets are posted there daily and, additionally, automatically pushed to the registered prediction servers.

Are all targets in CASP16 intended for prediction by all groups?
Targets for protein structure prediction will be divided into two tracks: those intended for prediction by all groups (i.e., both - human-expert and server groups), and those intended for fully automatic servers only. Human-expert groups predicting tertiary or/and quaternary structure should concentrate on all-group targets, while server groups should predict all targets. Accuracy estimates should be submitted for all quaternary structure prediction targets (assembly). Targets in RNA, ligand and ensembles categories should be approached by specialists in that area.

How protein structure targets are assigned to different tracks?
Assignment of a target to a particular track is made by the organizers and communicated to the predictors through the Target List page. Priority for inclusion in the all-group track is given to targets with low sequence identity to known proteins.

Are prediction time windows for all-group targets and server targets the same?
All-group targets are usually released with the 3-week prediction deadline, while server only targets usually have 72 hour prediction deadline. All targets are assigned two expiration dates (one - for server predictors and another - for human-expert groups). Accuracy estimates are typically requested two days after structure predictions are collected. More on the dealines and formats - in CASP16 format page.

When do you stop accepting submissions?
All predictions must be received and accepted before noon, 12pm PDT on the corresponding expiration date.

When targets are released?
Targets are released on business days only, around 9am PDT. They are released in batches of not more than 3 targets per day for servers and, usually, one target per day for expert groups. Data for model accuracy estimates category are released at noon, PDT. Sequence and other relevant information about the targets is posted at the Target List web page. Requests to the participating servers are sent shortly after the target release.

How many targets do you expect in CASP16?
In a typical 13-week target release window, we are planning to release 50-100 targets (depending on the availability) for tertiary structure prediction, 30-50 targets for assembly prediction, and as many relevant targets as we can get for other prediction categories.

I am a predictor of tertiary structure. Should I predict all targets?
No, unless you participate as a server group. If you are a human-expert group, you should concentrate on all-group targets.

I am a predictor of quaternary structure and complexes (Assembly category). How can I know if the target is a monomer or a multimer? Should I predict all targets?
In the first round of prediction, we will request modelers to submit their estimates of target's stoichiometry. After this, we will provide predictors with the information on the oligomerization state of the target, if known to the organizers (column Oligo in the Target List). Predictors in the Assembly category are encouraged to send their models for all submitted targets (including server-only ones) before human expiration deadline.

I am an estimator of model accuracy. Should I predict all multimeric targets?
Yes, both human-expert and server groups should predict accuracy of provided 3D server models for all multimeric targets. Deadlines for predictions in EMA (a.k.a. QA) category are the same for expert and server groups (2 days).

I participate in CASP as an expert group. Can I use server predictions submitted to CASP as starting points for my method(s)?
Yes, you can (obviously, with the proper acknowledgement of the original prediction). We will be releasing server predictions from selected groups soon after they are collected.

How many predictions can I submit?
A team may submit up to five models in the tertiary structure prediction and quaternary structure prediction categories. In the estimation of model accuracy category, predictors may submit one model.

Protein Structure Prediction Center
Sponsored by the US National Institute of General Medical Sciences (NIH/NIGMS)
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