Set Covalent Biding

Covalent Binding

Covalent Binding is a feature that predicts the potential for covalent bond formation between a protein and individual molecules by explicitly defining the Warhead and Product form for each molecule.

It is used when you want to:

• Evaluate a specific molecule

• Assume a specific Warhead reaction

• Define a clear binding outcome (Product form)

• Perform precise covalent binding predictions

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1. Activate a Covalent Protein

• Navigate to Bench.

• Activate the covalent-type protein to be used in the experiment.

Covalent Binding can only be executed when a covalent protein is activated.

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2. Select Molecules and Run Hyper Binding

• Click the Run Hyper Binding button for the molecule you want to analyze using Covalent Binding.

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3. Configure the Warhead

• In the configuration window, select the molecular region to be used as the Warhead.

• The Product form is generated based on the selected Warhead.

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4. Select a Product Form

• Review the list of Product forms generated based on the selected Warhead.

• Select the Product form to use for binding prediction.

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5. Add a Product Form Manually (Optional)

If the desired Product form is not provided, you can define one manually.

How to Add a Product Form

• Click Add Product Form.

• Review the following information in the configuration panel:

  • Target residue

  • Molecular structure

  
• Draw the Product form by connecting the residue to the molecular structure.

• Once configuration is complete, click Add.

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6. Final Product Form Selection

• Select one Product form from either:

  • the provided Product forms, or

  • the manually added Product forms.

Covalent Binding calculations are performed based on the selected Product form.

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7. Review Binding Calculation Results

• After the calculation is complete, you can review the Binding score.

• Covalent binding potential is provided as a numerical value based on the selected Warhead and Product form.

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8. Review Warhead Information

• Applied Warhead information can be reviewed in Bench fields.

• Enable Add Field > Covalent > Warhead.

• The Warhead applied to each molecule will be displayed in the table.