CCD - Main

Welcome

CRISPR-Cas-Docker (CCD) is for in silico docking experiments of CRISPR RNAs (crRNAs) and Cas proteins. It predicts RNA-protein interactions when your genomes have multiple CRISPR arrays and Cas systems. You can either provide experimental 3D structures of your crRNA and Cas protein or use 3D-predicted crRNA and AlphaFold-predicted Cas proteins.

Click here to complete the form below with an example

Step 1: Enter your query information

Your result will be linked to your email and your query name. Please write your query name less than 20 characters in alphabets, numbers, or underscores.

Email address:

Query name:

Step 2: Upload your Cas protein sequence

Directly upload ".fasta" format file (single file at once) or paste your Cas protein sequence below to run Alphafold2. (Important: protein sequences in capital letters, no fasta header)

Upload .pdb file instead of running alphafold

Step 3: Upload your CRISPR RNA sequence

Directly upload ".fasta" format file (single file at once) or paste your RNA sequence below to run RNAFold and RoseTTAFold. (Important: no fasta header)

Upload .pdb file instead of RNA sequence

References:

H. Park, J. Won, Y. Park, E. T. Anzaku, J. Vankerschaver, A. Van Messem, W. De Neve, H. Shim. CRISPR-CasDocker: Web-based in silico docking and machine learning-based classification for crRNAs and Cas proteins (bioRxiv link)
H. Park*, Y. Park*, U. Berani, E. Bang, J. Vankerschaver, A. Van Messem, W. De Neve, H. Shim. In silico optimization of RNA-protein interactions for CRISPR-Cas13-based antimicrobials. Biology Direct 17:1, 1-16 (2022). *authors contributed equally https://rdcu.be/c2qK8

If you use the results from CCD as part of published research, please also cite:

Yan Y, Tao H, He J, Huang S-Y.* The HDOCK server for integrated protein-protein docking. Nature Protocols, 2020; doi: https://doi.org/10.1038/s41596-020-0312-x.
Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021). https://doi.org/10.1038/s41586-021-03819-2
Lorenz, Ronny and Bernhart, Stephan H. and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L. ViennaRNA Package 2.0 Algorithms for Molecular Biology, 6:1 26, 2011, doi:10.1186/1748-7188-6-26
Cheng, C. Y., Chou, F. C., & Das, R. (2015). Modeling complex RNA tertiary folds with Rosetta. In Methods in enzymology (Vol. 553, pp. 35-64). Academic Press, doi:10.1016/bs.mie.2014.10.051