Use RFdiffusion-v2

The PDB structure of the protein you want to design a binder for, scaffold on, or partially diffuse. Please ensure this PDB file has chain IDs. An input PDB is REQUIRED for binder design, scaffolding, and partial diffusion.

Desired number of diffuser timesteps to generate your structure. Lower numbers produce lower quality results but have the advantage of taking less time. Recent improvements have allowed us to reduce the number of timesteps we need to use at inference time. In many cases, 20 steps provides outputs of equivalent quality to running with 200 steps (providing a 10X speedup). The default used by the RFdiffusion authors is now set to 50 steps, the former default was 200.

Check this option to use the "beta" model parameters for a better SSE balance. Useful if you are seeing lots of helices.

The target chain for the binder design experiment. This input is required if you are performing a binder design experiment.

The starting residue for the residues in range of your desired binding pocket target. If you are looking to design a binder for your input structure within range of residue 65 to 100, set this value to 65. To disable cropping set Binding Pocket Residue Start and Binding Pocket Residue End to 1.

The final residue for the residues in range of your desired binding pocket target. If you are looking to design a binder for your input structure within range of residue 65 to 100, set this value to 100. To disable cropping set Binding Pocket Residue Start and Binding Pocket Residue End to 1.

The minimum length of the designed binder. If you want your binder to be at least 10 residues long, set this value to 10.

The maximum length of the designed binder. If you want your binder to be at most 20 residues long, set this value to 20.

The model optionally readily learns that it should be making an interface which involving these hotspot residues. Input is ChainResidueNumber: A100 for residue 100 on chain A.

The target chain for scaffolding. This input is required if you are performing a scaffolding experiment.

The minimum amount to extend the Input Structure by N-Terminally.

The maximum amount to extend the Input Structure by N-Terminally.

The minimum amount to extend the Input Structure by C-Terminally.

The maximum amount to extend the Input Structure by C-Terminally.

The starting residue of the scaffold. Residues between Scaffold Start and Scaffold End will be preserved and extended from. Set both Scaffold Start and Scaffold End to 1 in order to preserve the entire structure as a scaffold.

The ending residue of the scaffold. Residues between Scaffold Start and Scaffold End will be preserved and extended from. Set both Scaffold Start and Scaffold End to 1 in order to preserve the entire structure as a scaffold.

The target chain for partial diffusion. This input is required if you are performing a partial diffusion experiment.

Specify the number of noising steps (only used for the partial diffusion protocol).

The beginning of the sequence region you want to keep fixed. The rest of the sequence will be noised. If you want to fix residues 1 to 10 set this value to 1. If you want to redesign the entire structure set this to 1.

The end of the sequence region you want to keep fixed. The rest of the sequence will be noised. If you want to fix residues 1 to 10 set this value to 10. If you want to redesign the entire structure set this to 1.

The desired length of the unconditionally generated protein. If you enter 100 the monomeric (order 1) protein will be 100 residues long. If you enter an order greater than 1 the protein will be that order multilpied by the length you specify.

Select the symmetrical design you want to use to predict your structure. Setting this to "auto" enables automatic symmetry dectection with AnAnaS.

Defines the number of copies in the symmetries. Think of it was the desired number of subunits in the predicted structure. This option will be ignored for Tetrahedral, Octahedral, and Icosahedral.

Generates compact structures by minimizing the radius of gyration (ROG) of the Cα atoms. Can be only be used for unconditional generation, motif scaffolding, and partial diffusion.

Encourages the formation of contacts within a monomeric protein. Can only be used for unconditional generation, motif scaffolding, and partial diffusion.

Encourages the formation of contacts within a multimeric protein. Can only be used for unconditional symmetric generation.

Used for motif scaffolding, where the goal is to design a protein structure around a given functional motif. The potential mimics interactions between the designed protein and a virtual substrate or ligand, encouraging the formation of a binding site that accommodates the motif. This option requires a ligand / substrate to be included the uploaded structure.

User for designing protein binders. It encourages the model to generate compact structures for the binder region by minimizing the radius of gyration (ROG) of the Cα atoms in the binder. A smaller ROG indicates a more compact binder structure.

User for designing protein binders. Encourages the formation of contacts within the binder region and at the interface between the binder and the target protein, respectively. Favors structures with more contacts, which can contribute to the stability and specificity of the binder-target interaction. Can only be used for binder design.