Instructions
1. (Optional) Create your JSON configuration file
Default configuration is available if you skip this step.
- Set your simulation parameters and generate the JSON config file. A unique identifier will be assigned (e.g.,
chai_{run_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. (Optional) Upload a FASTA file with your molecule sequence
Default FASTA files are available if you skip this step.
- Write your FASTA content and create the file. A unique identifier will be assigned (e.g.,
chai_{run_id}_input.fasta). - 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.
4. Click the "Run" button to start the simulation
5. View the 3D visualization of your molecule
Simulation parameters choice
If no config or fasta files are created, default values are chosen:
- chai1_default_input.fasta
- chai1_quick_inference.json
The files content is diplayed at the bottom of the page. The default json configuration makes the computation fast (about 2min) but results can be disappointing. Please use chai1_default_inference.json to have a wonderful protein 😃.
- chai1_quick_inference.json
{
"num_trunk_recycles": 1,
"num_diffn_timesteps": 10,
"seed": 42,
"use_esm_embeddings": true
"use_msa_server": false
}
Contact
For any issues or questions, please contact the developer or refer to the documentation.