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Antibody design using IgGM model. Use this skill when: (1) Epitope-conditioned de novo antibody design, (2) Antibody affinity maturation, (3) Using antigen PDB structure and epitope information. For binding affinity evaluation, use prodigy.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
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SOC 職業分類に基づく
| name | antibody-design-iggm |
| description | Antibody design using IgGM model. Use this skill when: (1) Epitope-conditioned de novo antibody design, (2) Antibody affinity maturation, (3) Using antigen PDB structure and epitope information. For binding affinity evaluation, use prodigy. |
| license | MIT |
| category | design-tools |
| tags | ["structure-design","sequence-design","antibody","nanobody"] |
| Requirement | Minimum | Recommended |
|---|---|---|
| Python | 3.10+ | 3.10 |
| CUDA | 11.7+ | 11.8 |
| GPU VRAM | 24GB | 80GB (A800) |
| RAM | 32GB | 64GB |
git clone https://github.com/TencentAI4S/IgGM.git
cd IgGM
pip install torch==2.0.1 --index-url https://download.pytorch.org/whl/cu118
pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.0.1+cu118.html
pip install tqdm requests numpy==1.23.5 termcolor==2.4.0 biopython==1.79 openmm==8.2 pdbfixer ml-collections==0.1.1
python design.py --fasta complex_sequence.fasta --antigen complex_structure.pdb --cal_epitope
# --antigen: the structure of a known complex
# --fasta: the sequence of a known complex
python design.py --fasta design_requirement.fasta --antigen antigen_structure.pdb --epitope 7 8 9 10 11 --output output_dir
# --fasta: Directory path to input design requirement FASTA files, X for design region
# --antigen: Directory path to input antigen PDB files
# --epitope: epitope residues in antigen chain A , for example: 7 8 9 10 11
# --output: Directory path to output PDB files
python design.py --fasta design_requirement.fasta --antigen antigen_structure.pdb --fasta_origin original_antibody_sequence.fasta --run_task affinity_maturation --num_samples 10 --output output_dir
# --fasta: Directory path to input design requirement FASTA files, X for design region
# --antigen: Directory path to input antigen PDB files
# --fasta_origin: Directory path to original antibody FASTA files for affinity maturation
# --num_samples: number of samples for residue
# --output: Directory path to output PDB files
>H # Heavy chain ID
VQLVESGGGLVQPGGSLRLSCAASXXXXXXXYMNWVRQAPGKGLEWVSVVXXXXXTFYTDSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARXXXXXXXXXXXXXXWGQGTMVTVSS
>L # Light chain ID
DIQMTQSPSSLSASVGDRVSITCXXXXXXXXXXXWYQQKPGKAPKLLISXXXXXXXGVPSRFSGSGSGTDFTLTITSLQPEDFATYYCXXXXXXXXXXXFGGGTKVEIK
>A # Antigen ID, needs to be consistent with the pdb file
NLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGP
output_dir/
├── antibody_0.fasta # designed antibody sequence (fasta file)
├── antibody_0.pdb # designed antigen-antibody complex structure (pdb file)
├── antibody_1.fasta
├── antibody_1.pdb
└── ...
Should I use IgGM?
│
└─ What type of design?
├─ Antibody de novo design → IgGM ✓
├─ Nanobody de novo design → IgGM ✓
└─ Binder design for general protein binder → boltzgen
Next: Evaluate binding affinity with prodigy.