Importing Protein

There are three ways to import protein

METHOD 1. Enter the PDB ID to register protein information

• If the 3D structure of the protein has been determined (e.g., via X-ray, Cryo-EM, NMR), you can enter the PDB ID to retrieve the information.

1. To register the protein structure, click Add.

1. You can choose PDB in Type

1. Enter the PDB ID in the ID field. You can find the PDB ID on the RCSB website.

1. When you click the Search button, you can view the 3D structure of the protein, as well as information about the chains and small molecules that compose the protein.

METHOD 2. Register protein information from AlphaFold database

• If the 3D structure of the protein has not been experimentally determined, you can use a predicted structure instead. These predicted structures are stored in the AlphaFold webpage.

1. To register the protein structure, click on Add protein structure.

1. You can choose AlphaFold in Type

1. Enter the UniProt ID in the ID field. You can find UniProt ID on the UniProt website.

Since Alphafold structures do not represent drug-bound protein conformations, they do not provide information on drug structural details or binding sites. Therefore, when using Alphafold structures, users must manually define the binding sites (determining binding site). Additionally, for proteins that undergo significant conformational changes upon drug binding, Alphafold may not be suitable for predicting drug-bound structures.

METHOD 3. Direct upload PDB file to register

• If you want to use private protein structures or structures that you have modified for specific purposes, you can upload the structure file directly.

1. To register the protein structure, click on Add protein structure.

1. You can choose Upload in Type

1. Select the PDB file from your device.

If you need to work with modified protein structures, such as those created through in silico point mutations, you can upload the structure file directly using this method.