Covalent sequence type protien

Protein Registration (Covalent · Sequence)

In covalent research, you can register sequence-based proteins to perform more flexible structure prediction and covalent binding analysis, including Co-folding.

This guide explains, step by step, how to register a Covalent (Sequence)–type protein.

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1. Access the Protein Management Menu

1. From the top navigation menu, go to Protein Management.

   
2. Click Add Protein.

3. In the protein type selection screen, choose Covalent (Sequence).

   
4. Click Done.

You will be taken to the Covalent Sequence protein registration screen.

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2. Overview: How to Add a Sequence Protein

Sequence-type proteins can be added using one of the following two methods:

1. Add a chain by searching for a protein

2. Add a chain manually

Please choose the method that best fits your research context and available information.

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Method 1. Add a Chain by Searching for a Protein

This method adds a chain by searching based on known protein information. It is suitable when you know identifiers such as the gene name or protein name.

Step-by-step

1. Click Add Protein.

2. Set the registration type to Covalent Sequence.

   
3. Click Search and Add Protein.

   
4. Enter information for the protein you want to add. You can search using:

• Protein name

• Gene name

• Organism

• UniProt ID

• PDB ID

1. Select the desired protein from the search results and click Next.

2. For the selected protein, the following options are provided:

• Mutation

• PTM

• Coenzyme

• Other structural options

Example 3D structures are displayed for each option. Options are ranked higher when the ligand is more likely to be an active compound.

1. Select the protein with the desired option values and click Next.

2. Review the detailed information for the selected protein.

   
3. Click Add.

4. Review the added protein chain information.

5. Set the Target residue.

• The Target residue can be set for only one protein chain among all chains.

1. Confirm the protein name and click Save.

Protein registration is complete.

After calculation is finished, you can activate the registered protein to run AI experiments.

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Method 2. Add a Chain Manually

If you already know the sequence information, you can manually add chains to register a protein. This method is suitable for custom proteins or designed sequences.

Step-by-step

Select Chain Type

1. In the chain addition area, select a Type. The following chain types are supported:

• Protein

• RNA

• DNA

• Coenzyme

• Inorganic ion

Select the appropriate chain type to add.

1. Set the Copies value. If multiple identical chains are required, you can add them using a single chain definition by setting the number of copies.

2. Enter information based on the selected chain type:

• Protein / RNA / DNA: Enter sequence information

• Coenzyme: Enter SMILES

• Inorganic ion: Select ion information

1. Set the Target residue.

• Can be set for only one protein chain among all chains

• This is the key residue where the covalent bond is formed

1. If needed, configure PTM & Modification:

   1. Under the Protein-type chain, click PTM & Modification.

   2. Select the amino acid for PTM.

   3. Choose the desired option from the provided PTM list.

   4. Review the selection and click Confirm.

   
2. Enter the protein name.

3. Click Save.

Protein registration is complete.

After calculation is finished, you can activate the registered protein to run AI experiments.