is a collective experiment for blind RNA structure prediction.
The sequence of a solved RNA structure is confidentially communicated to participating modelling groups a couple of weeks prior to publication. The results are assessed and presented in common publications involving structuralists and modellers.
Aims of the project
To determine the capabilities and limitations of current computational methods of 3D RNA structure prediction based on sequence;
To assess progress made and to improve assessment protocols and methods;
To identify whether there are specific bottlenecks that hold back progress;
To promote the available methods and guide potential users in the choice of suitable tools;
To encourage the RNA structure prediction community in their efforts to improve the current tools and to make automated prediction tools available;
To explore the underlying mechanism of ligand-RNA binding and associated conformational changes.
Confidential agreement required from new users: "I will use the provided sequence data for prediction purposes only. I will not distribute the sequences in any form outside my working group."
It is strongly recommended to avoid assessment error that all the predictions be formatted in standard PDB format. We provide a python script here for generating standard PDB format files into which the coordinates need to be replaced by the predictors.
Please name the submission file without space in the file name. The suggested names are: PZ#_Method.pdb for web servers and PZ#_GroupName.pdb for human predictors.
RNA chains should be named in alphabetical order: A for the first chain, B for the second chain, and so on.
Up to FIVE prediction models should be submitted as the final results for each puzzle from each prediction method. Each prediction group can submit results from several prediction methods (automatic or manual, etc.).
Please put all prediction models together in one PDB file as in the NMR format (Separate models by lines: "MODEL n" and "ENDMDL").
For submission, please either use the online registration and submission portal (see the open-puzzle tag: http://www.rnapuzzles.org/open-puzzle/) or send us an email (Please send an email to firstname.lastname@example.org and cc. email@example.com).
For structure comparison metrics, please refer to RNA-Puzzles toolkit at https://chichaumiau.github.io/rnapuzzlestoolkit. Please find the reference at Nucleic Acids Res. 2020 Jan 24;48(2):576-588. To use evaluation metrics in CASP15, please also refer to the repos: https://github.com/philpham8/casp-pipeline and https://github.com/DasLab/CASP15_RNA_EM. The reference can be found at biorxiv.
Call for participants
We hope more structural biologists can help us in providing more crystallographic, cryo-EM or NMR structures. Any kind of RNA related structure information is encouraged. Anyone who may have a RNA structure ready for publication please contact us (Please send an email to firstname.lastname@example.org and cc. email@example.com).
We encourage more predictors who are interested in RNA structure prediction to take part in this compitition to push forward the field. Anyone who is interested please send us an email (Please send an email to firstname.lastname@example.org and cc. email@example.com).