### 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:**
```fasta
>{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):**
```fasta
>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:**
```fasta
>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.