How to run an Epitope Mapping job
Epitope Mapping requires structural models as input. Upload existing .PDB models or work from a de novo Alpha Fold model or immunebuilder.
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Step 1. On the LensAI™ Home Page, click "Run Analysis"
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Step 2. Locate the Epitope Mapping analysis and click "Run Job"
- Step 3. Inside the run configuration, select the input datasets for the receptor and the ligand
Caution: The dataset must be chosen, not the .pdb file itself.
- Step 4. Define the output dataset logical name
Caution: The name of the output dataset should not contains any space. Underscore is accepted.
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Step 5. Configure the other inputs
- receptor_chains: Define the chain identifiers in the PDB file of the target you want to include or exclude from the analysis. By specifying the chains of interest, you can focus your analysis on particular receptor or ligand components, allowing for a more targeted investigation of their interactions. Additionally, excluding irrelevant chains can help streamline the computation process, reduce noise in the results, and enhance the clarity of your findings. Make sure to carefully review the chains in your model to ensure that your selections align with your research objectives. Use capitals and do not comma separate.
Using Immubuilder models? Your chains are identified as H or L. Including both: HL
Using PDB models? Most often chains are alphabetical; A,B,C. Including all chains: ABC
- ligand_chains: Define the chain identifiers in the PDB file of the antibody you want to include or exclude from the analysis. Use capitals and do not comma separate.
- global_docking_poses: Number of docking poses to generate in the global docking step
- global_docking_poses_to_keep: Number of docking poses to keep after the global docking step
- constrain_on_paratope: Perform paratope prediction and bias docking towards paratope being in contact with target
- local_docking_clusters: Number of clusters from global docking to examine with local docking
- clustering_method: Method used to cluster poses from global docking and examine with local docking
- local_docking_poses: Number of docking poses to generate in the local docking step
- local_docking_poses_to_keep: Number of docking poses to keep after the local docking step
- receptor_chains: Define the chain identifiers in the PDB file of the target you want to include or exclude from the analysis. By specifying the chains of interest, you can focus your analysis on particular receptor or ligand components, allowing for a more targeted investigation of their interactions. Additionally, excluding irrelevant chains can help streamline the computation process, reduce noise in the results, and enhance the clarity of your findings. Make sure to carefully review the chains in your model to ensure that your selections align with your research objectives. Use capitals and do not comma separate.
- Step 6. Optionally provide experiment details under the General Run Metadata Inputs
- Step 7. Click "Run Job" to launch the application
- Step 8. Monitor the state and the results of the analysis in the "Applications" page under the "History" tab
