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Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts, (4) Choosing between SPR vs BLI platforms.
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SOC 職業分類に基づく
Computational protein design toolkit. Use this skill group when: (1) Designing protein binders from scratch, (2) Predicting protein structures (Chai, Boltz, Protenix), (3) Sequence design with ProteinMPNN/LigandMPNN/SolubleMPNN, (4) Quality control and filtering of protein designs, (5) Planning and managing binder design campaigns, (6) Experimental characterization (SPR, BLI, cell-free expression), (7) Searching protein databases (PDB, UniProt, AFDB), (8) Antibody/nanobody design (IgGM, mBER). This is the top-level index. Sub-skills handle specific tools.
Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen or BindCraft, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types.
Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-source alternative to AF2, (4) Predicting protein-ligand complexes, (5) Using local GPU resources. For QC thresholds, use protein-qc. For AlphaFold2 prediction, use alphafold. For Chai prediction, use chai.
All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small molecules or ligands, (3) Want all-atom diffusion (not just backbone), (4) Require precise binding geometries, (5) Using YAML-based configuration. For sequence-only design, use proteinmpnn. For structure validation, use boltz.
Goal-oriented binder design campaign planning and health assessment. Use this skill when: (1) Planning a complete binder design campaign, (2) Converting high-level goals into runnable pipelines, (3) Assessing campaign health and pass rates, (4) Diagnosing why designs are failing QC, (5) Estimating time, cost, and expected yields, (6) Selecting between design tools for a specific target. This skill orchestrates the other protein design tools.
Guidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggregation, (3) Optimizing DNA template design for CFPS, (4) Expressing difficult proteins (disulfide-rich, toxic, membrane).
| name | binding-characterization |
| description | Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts, (4) Choosing between SPR vs BLI platforms. |
| license | MIT |
| category | experimental |
| tags | ["binding","spr","bli","validation"] |
| source | https://github.com/adaptyvbio/protein-design-skills |
| Factor | Choose SPR | Choose BLI |
|---|---|---|
| Sensitivity | Small molecules (<500 Da) | Large complexes, antibodies |
| Throughput | Low-medium (serial) | High (96-well parallel) |
| Sample purity | Required (clogs fluidics) | Tolerates crude lysates |
| Kinetic resolution | Higher (fast kinetics) | Lower |
| Mass transport | More sensitive | Less sensitive |
| Maintenance | High (fluidics) | Low (dip-and-read) |
| Problem | Mechanism | Solution |
|---|---|---|
| Hydrophobic CDRs adsorb to SPR surface | Gold/dextran surface | Add 0.05% Tween-20, use CM7 chip |
| Aggregation in SPR fluidics | Mass transport artifacts | Filter sample (0.22μm), reduce ligand density |
| Protein degrades during continuous flow | High instability | Shorter cycle time, add trehalose 5% |
| Small analyte (<10 kDa) on BLI | Low signal | Use SPR instead |
| Weak affinity (KD >10μM) on BLI | Fast dissociation | Increase analyte concentration |
| Condition | Targets | Caution |
|---|---|---|
| 10 mM Glycine pH 2.0-2.5 | Most protein-protein | May denature ligand |
| 1-2 M NaCl | Ionic interactions | Mild, try first |
| 10 mM NaOH | Very stable ligands | Can hydrolyze proteins |
| 10 mM EDTA | His-tag, metal-dependent | Strips Ni-NTA |
