Antibody-Antigen Docking¶
Antibody-antigen docking is the task of predicting the structure of an antibody-antigen complex given its sequence. In practice, top \(K\) predictions will be returned to account for the uncertainty in the epitope location.
Challenges¶
The huge size of the protein system makes it extremely difficult to determine the optimal orientation of two proteins. Moreover, the flexible regions of the two proteins often undergo conformational changes during docking. Rigid docking algorithms cannot adapt to such real-world scenarios.
Features¶
- State-of-the-art algorithm: Empowered by the latest geometric deep learning techniques and large-scale structural pretraining, GeoAbDock exhibits powerful and robust performance on antibody-antigen docking.
- Flexible docking supported: GeoAbDock considers the conformational changes of flexible regions during docking. It also supports generating multiple candidate poses and scoring them. Compared with rigid docking, it is more suitable for real-world use cases.
- Cloud-based, mass-scale: Support batched prediction and relaxation of multiple sequences on our cloud platform. Enjoy high accuracy and high efficiency at the same time!
- Easy to use: Only need the antigen and antibody sequences as input. The predicted structures are clustered to visualize the epitope more clearly.
Inputs¶
To submit an Antibody-Antigen Docking job, open the Project Editor and select "Antibody-Antigen Docking" from the "Structure Modeling" dropdown menu.
- Complex: The complex sequence.
- Sequence: Sequence of an antibody-antigen complex. The overall number of residues shall not exceed 1200 residues.
>6xc3_C NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIR GDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVNYNYLYRLFRKSNLKPFERDISTEIYQA GSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK >6xc3_H QMQLVQSGTEVKKPGESLKISCKGSGYGFITYWIGWVRQMPGKGLEWMGIIYPGDSETRYSPSFQGQVTI SADKSINTAYLQWSSLKASDTAIYYCAGGSGISTPMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGG TAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSN TKVDKKVEPKSC >6xc3_L DIQLTQSPDSLAVSLGERATINCKSSQSVLYSSINKNYLAWYQQKPGQPPKLLIYWASTRESGVPDRFSG SGSGTDFTLTISSLQAEDVAVYYCQQYYSTPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVC LLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSP VTKSFNRGECS
- (Upload Sequence): Upload your own antibodies (a .FASTA file) by clicking the "" button. You can only upload FASTA files with one antibody-antigen complex. The FASTA labels of the chains in the complex must have the same prefix and end with
_{chain_id}
. Above is an example.
- Sequence: Sequence of an antibody-antigen complex. The overall number of residues shall not exceed 1200 residues.
- Job Name: Name of the job. Note that the job name must be unique within the project.
Models & Parameters¶
GeoAbDockv4, our proprietary antibody-antigen docking model, is available for this job. Parameters of the model are as follows.
- Mode: Choose from "fast" or "accurate". Accurate mode samples more poses and has a higher docking success rate.
Results¶
Click the job name in the Files & Jobs panel to view the job results. The result summary is stored in a CSV file, which can be downloaded by clicking the "" button to the top-right of the Summary Table.
The summary table contains the following columns:
- rank: Rank of the pose starting from 0, sorted by the model's confidence score in descending order.
- score: wpTM score of the predicted structure (from 0 to 1) indicating the confidence in the prediction. It is calculated by \(\text{wpTM} = 0.8 \times \text{ipTM} + 0.2 \times \text{pTM}\).
In the rightmost column, you could click on the "" button to view the predicted structure.