Genie 2

Runs inference of a Genie 2 model for protein generation, supporting both unconditional and motif/multimotif scaffolding. Fully reproducible, with flexible control over sequence length and motif placement.

Quick Start

1. Select the desired checkpoint (40-epoch for unconditional, 30-epoch for motif scaffolding).
2. Set minimum and maximum sequence lengths.
3. (Optional) Provide input PDB and contigs for motif scaffolding.
4. Run the node to generate protein structures.

Setup Guide

1. Unconditional Generation

1. Leave input_pdb and contigs empty.
2. Set min_length, max_length, and length_step for desired sequence range.
3. Choose checkpoint (recommended: 40-epoch).

2. Motif/Multimotif Scaffolding

1. Provide an input_pdb containing the motif(s).
2. Define contigs to specify motif and flexible regions (e.g., A367-372/10-10/A342-348).
3. Set min_length and max_length (used for motif scaffolding as well).
4. Choose checkpoint (recommended: 30-epoch).

Basic Usage

Unconditional Generation

• Generate proteins of varying lengths without motifs.
• Use for de novo protein design.

Motif Scaffolding

• Scaffold one or more motifs into generated proteins.
• Specify motif positions and flexible regions using contigs.

Configuration

Required Inputs

Field	Description	Type	Example
checkpoint	Checkpoint name. Use 40-epoch for unconditional, 30-epoch for motif scaffolding.	COMBO	base/epoch.40
scale	Sampling noise scale.	FLOAT	0.6
batch_size	Batch size. Reduce if running out of GPU memory.	INT	1
min_length	Minimum sequence length.	INT	100
max_length	Maximum sequence length.	INT	100
length_step	Sequence length step size (unconditional only).	INT	5
contigs	Scaffold structure: fixed motifs (A10-25), flexible regions (5-15), explicit motif groups (A, B, etc.). See Setup Guide for format.	STRING	A367-372/10-10/A342-348
seed	Base seed for randomness.	INT	42

Optional Inputs

Field	Description	Type	Example
input_pdb	Initial PDB to start generation from (scaffolding)	PDB	{"motif1": "...PDB..."}

Outputs

Field	Description	Example
generation.pdb	Generation result.	{"design_0": "..."}
motif.pdb	Generation motif pdb.	{"motif1": "..."}

Best Practices

Checkpoint Selection

• Use 40-epoch checkpoint for unconditional generation.
• Use 30-epoch checkpoint for motif/multimotif scaffolding.

Contigs Formatting

• For motif scaffolding, clearly define motif and flexible regions in contigs.
• Use explicit motif groups (A, B, etc.) for multimotif tasks.

Troubleshooting

Common Issues

• No lengths generated: Ensure min_length ≤ max_length and length_step is positive.
• Missing contigs for scaffolding: For motif scaffolding, both input_pdb and contigs must be provided.
• Chain breaks not supported: All segments in contigs are sequentially connected; do not use chain breaks.

Need Help?

• Contact support for further assistance.