Use RFdiffusion2

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BETA Protein Design Enzymes Peptides Proteins

Overview

RFdiffusion2 is a deep generative method that enables the design of enzymes directly from sequence-agnostic, atom-level descriptions of their active sites (theozymes). It overcomes previous limitations by simultaneously inferring appropriate side-chain rotamers and sequence positions for catalytic residues, eliminating the need for computationally intensive enumeration steps.

Neurosnap Overview

The RFdiffusion2 online webserver allows anybody with a Neurosnap account to run and access RFdiffusion2, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong terms of service and privacy policy.

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Features

  • Atom-level active site scaffolding
  • Unindexed (sequence-agnostic) motif scaffolding
  • Simultaneous rotamer and scaffold inference
  • Conditioning on ligand functional groups
  • Generation of full ligand conformers from partial structures

Statistics

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API Request

Access RFdiffusion2 using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.

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Job Note

Provide a name or description for your job to help you organize and track its results. This input is solely for organizational purposes and does not impact the outcome of the job.

Configuration & Options

Service Inputs

Upload the PDB structure to use as the template for design. Must have chain IDs.

Contig String Instructions

A contig string defines which regions of your input PDB are fixed (motifs) and which are generated (inpaint).

  • Motif segment: - or
    • Example: A1-100 means residues 1 through 100 from chain A.
  • Inpaint segment: or -
    • Example: 20-30 means generate a segment of 20 to 30 residues.
  • Multi-chain: Use _ to separate output chains.
    • Example: A1-150_40-60 means chain A is fixed (1-150), chain B is generated (40-60 residues).
A10-30,20-30,A31-50
A1-150_40-60
  • You can mix motifs and inpaint segments as needed.
  • The order of segments defines the order in the output.
  • If unsure, start with a simple motif or inpaint example.

Contig string specifying fixed and generated regions. See instructions above.

Contig Atoms Instructions

Contig atoms let you constrain only specific atoms of a residue. This is useful for fixing the backbone while redesigning the sidechain, or for advanced motif scaffolding.

  • Format: : ATOM1,ATOM2,…
    • Example: A35: N,CA,C,O
    • Use * or all to specify all heavy atoms: A42: *
A35: N,CA,C,O
B12: CB,CG
C7: *
  • Atom names must match those in the PDB (N, CA, C, O, CB, etc.).
  • If you want to fix all atoms for a residue, use * or all.
  • If left blank, all atoms in motif regions will be fixed by default.

Specify atom-level constraints, one per line. See instructions above.

3-letter code for ligand (must match PDB if used). Ligands must be defined in the PDB with HETATM and CONECT records.

Minimum length for generated (inpaint) regions. Ignored if contigs is set. Use this to control the minimum size of inpainted regions.

Maximum length for generated (inpaint) regions. Ignored if contigs is set. Use this to control the maximum size of inpainted regions.

If checked, treat contigs as guideposts for inference.

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