M01 Ligand and Molecule Generator Tool

This application allows you to generate molecules and ligands based on your input. Follow the steps below to make the most of this tool.

Getting Started

1. Accessing the Tool

Open your web browser and navigate to the "https://m01tool.com/" URL. Then, click on "Ligand Generator" button. You should see a user-friendly interface with the title "M01 Web Tool".

2. Input Fields

The main interface consists of several input fields. Please fill them out carefully:

  • SMILES: Enter the SMILES (Simplified Molecular Input Line Entry System) representation of the molecule you want to analyze. By clicking on submit button, An image of the molecule you entered will be displayed. This visual representation will help you understand the structure better. You can select the atom number, that you want to make the connections from.
  • Connection Site: Specify the connection site of the molecule. This refers to a specific atom or group within the molecule that will interact with other molecules.
  • Terminal: Indicate the terminal group of the molecule. This helps define the end of the molecular structure. In a peptide chain it can be rather the end of the molecule which ends with a carboxyl group (C-terminal) or an amino group (N-terminal.
  • Sequence: Input the sequence of amino acids. This information is relevant for generating ligands that may include these amino acids. Each amino acid has two stereoisomers, mirror images of one another except for glycine. You can enter the amino acid sequence as any of these two kinds separately by their one-letter symbols.
  • Other Molecules (SMILES): If you want to include other molecules, enter their SMILES representations here, separated by commas.

3. Submitting the Form

Once you have filled in all the necessary fields, click on the Submit button. The application will process the information and generate the ligands based on your input.

4. Viewing Results

After submitting the form, you will see the generated ligands. The generated ligands will be displayed below the molecule structure. These are the ligands created by the tool based on your input.

5. Downloading Results

If you wish to keep a record of the generated ligands, you can download them in CSV format:

- Click the Download in CSV button, which will provide you with a CSV file containing the SMILES representations of the generated ligands.

Tips for Successful Input

Valid SMILES: Ensure that the SMILES representation you enter is valid. You can use tools like the RDKit library or online SMILES validators to check your input.

Amino Acid Sequences: When entering amino acid sequences, make sure you are using the correct notation (e.g., single-letter codes for amino acids).

Connection Site and Terminal: Clearly define the connection site and terminal groups, as they significantly influence the ligand generation process.

Troubleshooting

-If the application does not generate the expected results, double-check your inputs for any mistakes.

- Ensure your browser does not block any content that may prevent images from being displayed.

- If you encounter any errors, please reach out to the support team or check the GitHub repository for updates and issues.

Additional Resources

Visit our GitHub page for the source code and additional documentation or read the preprint article that discusses the tool and its applications. Thank you for using the M01 Web Tool! We hope it assists you in your molecular and ligand generation needs.