Registering a Covalent Target Protein (COV 3D Structure)
To start covalent research, you must first register a covalent-type target protein.
This guide explains, step by step, how to register a COV 3D Structure–type protein.
1. Access the Protein Management Menu
From the top navigation menu, go to Protein Management.
In the protein type selection screen, choose Covalent (3D Structure).
You will be taken to the COV 3D Structure protein registration screen.
2. How to Register a COV 3D Structure Protein
A COV 3D Structure protein can be registered using one of the following three methods:
Use the AlphaFold Database
Upload a PDB file directly
Please choose the method that best fits your research needs.
Method 1. Register a Protein Using a PDB ID
This method is suitable when using proteins with experimentally determined 3D structures
(e.g., X-ray crystallography, Cryo-EM, NMR).
Confirm that the registration type is Covalent 3D Structure.
Enter the PDB ID.
The PDB ID can be found on the RCSB PDB website.
You can review the following information:
The protein’s 3D structure
Included small molecules (ligands, cofactors, etc.)
After reviewing the structure, configure the Target residue.
The Target residue is the key residue where the covalent bond is formed and serves as the reference for all subsequent covalent screening and binding calculations.
Method 2. Register a Protein Using the AlphaFold Database
If an experimentally determined structure is not available, you can use a structure predicted by AlphaFold.
Confirm that the registration type is Covalent 3D Structure.
Select AlphaFold as the type.
Enter the UniProt ID.
The UniProt ID can be found on the UniProt website.
You can review:
The AlphaFold-predicted 3D protein structure
After reviewing the structure, configure the Target residue.
Notes on Using AlphaFold Structures
AlphaFold structures do not reflect ligand-bound conformations.
Binding site information is not included.
Users must manually define the binding site when using AlphaFold structures.
Method 3. Register a Protein by Uploading a PDB File
This method is suitable when using custom protein structures, such as internally generated or modified models.
Confirm that the registration type is 3D Structure.
Select Upload as the type.
Choose the PDB file from your device.
Once the upload is complete, review the structural information.
You can review:
The uploaded protein 3D structure
After reviewing the structure, configure the Target residue.
Example Use Cases
Structures generated via in silico point mutation
Protein structures with modified or refined binding sites
Custom protein structures maintained for internal research
In these cases, uploading a PDB file is the most appropriate approach.
