菜单
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.
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基于 SOC 职业分类
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Analyze potential drug-drug interactions (DDI) for up to 5 drugs using KEGG DDI database. Use this skill when: (1) Checking interactions between multiple medications, (2) Assessing DDI risk for drug combinations, (3) Understanding interaction mechanisms and severity, (4) Analyzing CYP enzyme involvement in DDIs.
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| 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.