introduction_page.md

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Gradio interface instructions

1. Create your JSON configuration file (Optional)

Default configuration is available if you skip this step.

• In the Configuration 📦 window, set your simulation parameters and generate the JSON config file. You can provide a file name in the dedicated box that will appear in the list of available configuration files. If you don't, a unique identifier will be assigned (e.g., chai_{unique_id}_config.json).
• Parameters:
  • Number of diffusion time steps: 1 to 500
  • Number of trunk recycles: 1 to 5
  • Seed: 1 to 100
  • ESM_embeddings: Include or not
  • MSA_server: Include or not

2. Upload a FASTA file with your molecule sequence (Optional)

Default FASTA files are available if you skip this step.

• In the Configuration 📦 window, write your FASTA content and create the file. You can provide a file name in the dedicated box that will appear in the list of available configuration files. If you don't provide a file name a unique identifier will be assigned (e.g., chai_{unique_id}_input.fasta). Also, if you don't provide a fasta content a default sequence will be written in the file.
• Warning: The header must be well formatted for Chai1 to process it.

FASTA template:

>{molecule_type}|{molecule_name}
Sequence (for protein/RNA/DNA) or SMILES for ligand

Accepted molecule types: protein/ rna/ dna / ligand

Default input (provided by Chai1):

>protein|name=example-of-long-protein
AGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDRETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHTLQWMFGCDLGPDGRLLRGYDQSAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKETLQRAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQWDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP

>protein|name=example-of-short-protein
AIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

>protein|name=example-peptide
GAAL

>ligand|name=example-ligand-as-smiles
CCCCCCCCCCCCCC(=O)O

For a peptide, use `protein` as the molecule type.

Other example:

>protein|lysozyme
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPDLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCAAINQVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPDRAKRVITTFRTGTWDAYKNL

3. Select your config and FASTA files

Files are stored in your working directory as you create them.

In the Run folding simulation 🚀 window, refresh the file list by clicking on the Refresh available files. Then select the configuration and fasta file you want.

4. Run the simulation

Press the Run Simulation button to start the folding simulation. Five biomolecules folding simulations will be performed. This parameter is hard coded in Chai-1. The simulation time is expected to be from 2min to 10min depending on the molecule.

5. Analyse the results of your simulation

To analyse the results of the simulation, two outputs are provided:

• A table showing the score of the 5 folding performed
• Interactive 3D visualization of the molecule

Finally, you can get to the Plot CIF file 💻 window to watch the cif files. This is mainly used to visualize CIF files after using this tool as an MCP server.