RFAntibody API

RFAntibody is a set of tools for the de novo design of antibodies. The system consists of specially tuned versions of RFDiffusion, ProteinMPNN, and AlphaFold2. These three tools are implemented as separate API services to allow for filtering and analysis between steps.

The RFAntibody pipeline is described in detail in this preprint

Command Line Interface

The three tools comprising the RFAntibody pipeline are implemented under the lev engine submit rf-antibody sub-command to distinguish them from their general purpose counterparts.

RFDiffusion

The RFAntibody RFDiffusion tool requires that the input antibody framework PDB be numbered using the Chothia numbering system.
Examples of antibody framework PDBs formatted in a way acceptable to RFAntibody RFDiffusion can be found in the SabDab Databse

RFAntibody RFDiffusion requires that PDB files be additionally annotated with standardized chain names and PDB REMARKlines indicating the residue indices of the CDR loops.
The RFDiffusion RFAntibody API automatically performs this annotation.

Examples

Below is an example of how to run RFAntibody using the lev command line application.

lev engine submit rf-antibody rf-diffusion \
    --target-pdb-file rsv_site3.pdb \
    --framework-pdb-file hu-4D5-8_Fv_clean.pdb \
    --heavy-chain H \
    --light-chain L \
    --custom-arguments='ppi.hotspot_res=[T305,T456]' \
    --custom-arguments=antibody.design_loops='[L1:8-13,L2:7,L3:9-11,H1:7,H2:6,H3:5-13]' \
    --custom-arguments=inference.num_designs=1000

Inputs

  • --target-pdb-file (str)
    • A PDB file of the desired binding target
  • --framework-pdb-file (str)
    • A PDB file of the desired antibody framework to design. PDB file must be numbered with Chothia numbering
  • --heavy-chain (str)
    • The chain ID of the heavy chain in the input PDB. Default is H
  • --light-chain (str)
    • The chain ID of the light chain in the input PDB. Default is L
  • --custom-arguments (str)
    • Custom arguments passed directly to RFDiffusion. See the command line example above for the appropriate way to use this flag. At least one custom argument should be provided to RFDiffusion, probably the antibody.design_loops argument.
  • --gpu-type (str)

Outputs

  • out
    • A directory containing all of the outputs from RFDiffusion

ProteinMPNN

The RFAntibody ProteinMPNN tool generates sequences for the CDR loops created by the RFAntibody RFDiffusion tool. Unlike the traditional ProteinMPNN method, RFAntibody ProteinMPNN generates PDB files rather than FASTA files

Examples

The following command will generate sequences for a set of pdb files produced by the RFAntibody RFDiffusion tool, using default settings

lev engine rf-antibody protein-mpnn out/*.pdb

Inputs

  • --pdb-file (str)
    • the path to one or more PDB files generated by RFAntibody RFDiffusion
  • --augment-epsilon (float)
  • --connections (int)
  • --gpu-type (string)
    • The GPU to run RFDiffusion on, valid options are t4, l4, and a100. Try using a100 if jobs modeling large targets fail. Default is t4
  • --loop-string
    • The set of loops to design. The Default is H1,H2,H3,L1,L2,L3
  • --n-mpnn-designs (int)
    • The number of designs to generate per input PDBs. The default is 1
  • --omit-aa (string)
    • Amino Acids to omit from design. The default is CX
  • --protein-features (string)
    • Protein Features to include in inference. The default is full
  • --sampling-temperature (float)
    • Sampling Temperature. The default is 0.000001

Outputs

  • out
    • A directory containing all of the outputs from ProteinMPNN

AlphaFold2

RFAntibody AlphaFold2 takes as input 1 or more PDB files produced by RFAntibody ProteinMPNN and predicts the structures of the CDR loops given the sequences generated by ProteinMPNN.

Examples

lev engine submit rf-antibody af2 out/*.pdb

Inputs

  • --pdb-file (str)
    • the path to one or more PDB files generated by RFAntibody RFDiffusion
  • --gpu-type (string)
    • The GPU to run RFDiffusion on, valid options are t4, l4, and a100. Try using a100 if jobs modeling large targets fail. Default is l4
  • --custom-arguments (str)
    • Custom arguments passed directly to AlphaFold2.

Outputs

  • out
    • A directory containing all of the outputs from AlphaFold2

Updated: