openbio

Required: OPENBIO_API_KEY environment variable.

```bash

export OPENBIO_API_KEY=your_key_here

```

Base URL: https://openbio.fly.dev/

```bash

# List available tools

curl -X GET "https://openbio.fly.dev/api/v1/tools" \

-H "X-API-Key: $OPENBIO_API_KEY"

# Get tool schema (always do this first!)

curl -X GET "https://openbio.fly.dev/api/v1/tools/{tool_name}" \

-H "X-API-Key: $OPENBIO_API_KEY"

# Invoke tool

curl -X POST "https://openbio.fly.dev/api/v1/tools" \

-H "X-API-Key: $OPENBIO_API_KEY" \

-F "tool_name=search_pubmed" \

-F 'params={"query": "CRISPR", "max_results": 5}'

```

```

What do you need?

│

├─ Protein/structure data?

│ └─ Read rules/protein-structure.md

│ → PDB, AlphaFold, UniProt tools

│

├─ Literature search?

│ └─ Read rules/literature.md

│ → PubMed, arXiv, bioRxiv, OpenAlex

│

├─ Genomics/variants?

│ └─ Read rules/genomics.md

│ → Ensembl, GWAS, VEP, GEO

│

├─ Small molecule analysis?

│ └─ Read rules/cheminformatics.md

│ → RDKit, PubChem, ChEMBL

│

├─ Cloning/PCR/assembly?

│ └─ Read rules/molecular-biology.md

│ → Primers, restriction, Gibson, Golden Gate

│

├─ Structure prediction/design?

│ └─ Read rules/structure-prediction.md

│ → Boltz, Chai, ProteinMPNN, LigandMPNN

│

├─ Pathway analysis?

│ └─ Read rules/pathway-analysis.md

│ → KEGG, Reactome, STRING

│

└─ Clinical/drug data?

└─ Read rules/clinical-data.md

→ ClinicalTrials, ClinVar, FDA, Open Targets

```

1. Always Check Tool Schema First

```bash

# Before invoking ANY tool:

curl -X GET "https://openbio.fly.dev/api/v1/tools/{tool_name}" \

-H "X-API-Key: $OPENBIO_API_KEY"

```

Parameter names vary (e.g., pdb_ids not pdb_id). Check schema to avoid errors.

2. Long-Running Jobs (submit_* tools)

Prediction tools return a job_id. Poll for completion:

```bash

# Check status

curl -X GET "https://openbio.fly.dev/api/v1/jobs/{job_id}/status" \

-H "X-API-Key: $OPENBIO_API_KEY"

# Get results with download URLs

curl -X GET "https://openbio.fly.dev/api/v1/jobs/{job_id}" \

-H "X-API-Key: $OPENBIO_API_KEY"

```

3. Quality Thresholds

Don't just retrieve data—interpret it:

AlphaFold pLDDT: > 70 = confident, < 50 = disordered

Experimental resolution: < 2.5 Å for binding sites

GWAS p-value: < 5×10⁻⁸ = genome-wide significant

Tanimoto similarity: > 0.7 = similar compounds

See individual rule files for detailed thresholds.

Read these for domain-specific knowledge:

Core API

| File | Description |

|------|-------------|

| [rules/api.md](rules/api.md) | Core endpoints, authentication, job management |

Data Access Tools

| File | Tools Covered |

|------|---------------|

| [rules/protein-structure.md](rules/protein-structure.md) | PDB, PDBe, AlphaFold, UniProt |

| [rules/literature.md](rules/literature.md) | PubMed, arXiv, bioRxiv, OpenAlex |

| [rules/genomics.md](rules/genomics.md) | Ensembl, ENA, Gene, GWAS, GEO |

| [rules/cheminformatics.md](rules/cheminformatics.md) | RDKit, PubChem, ChEMBL |

| [rules/molecular-biology.md](rules/molecular-biology.md) | Primers, PCR, restriction, assembly |

| [rules/pathway-analysis.md](rules/pathway-analysis.md) | KEGG, Reactome, STRING |

| [rules/clinical-data.md](rules/clinical-data.md) | ClinicalTrials, ClinVar, FDA |

ML Prediction Tools (Detailed)

| File | Tool | Use Case |

|------|------|----------|

| [rules/structure-prediction.md](rules/structure-prediction.md) | Index | Decision tree for all prediction tools |

| [rules/boltz.md](rules/boltz.md) | Boltz-2 | Structure + binding affinity |

| [rules/chai.md](rules/chai.md) | Chai-1 | Multi-modal (protein+ligand+RNA+glycan) |

| [rules/simplefold.md](rules/simplefold.md) | SimpleFold | Quick single-protein folding |

| [rules/proteinmpnn.md](rules/proteinmpnn.md) | ProteinMPNN | Fixed-backbone sequence design |

| [rules/ligandmpnn.md](rules/ligandmpnn.md) | LigandMPNN | Ligand-aware sequence design |

| [rules/thermompnn.md](rules/thermompnn.md) | ThermoMPNN | Stability (ΔΔG) prediction |

| [rules/geodock.md](rules/geodock.md) | GeoDock | Protein-protein docking |

| [rules/pinal.md](rules/pinal.md) | Pinal | De novo design from text |

| [rules/boltzgen.md](rules/boltzgen.md) | BoltzGen | End-to-end binder design |

| Category | Count | Examples |

|----------|-------|----------|

| Protein structure | 23 | fetch_pdb_metadata, get_alphafold_prediction |

| Literature | 14 | search_pubmed, arxiv_search, biorxiv_search_keywords |

| Genomics | 27 | lookup_gene, vep_predict, search_gwas_associations_by_trait |

| Cheminformatics | 20+ | calculate_molecular_properties, chembl_similarity_search |

| Molecular biology | 15 | design_primers, restriction_digest, assemble_gibson |

| Structure prediction | 15+ | submit_boltz_prediction, submit_proteinmpnn_prediction |

| Pathway analysis | 24 | analyze_gene_list, get_string_network |

| Clinical data | 22 | search_clinical_trials, search_clinvar |

1. Not checking schemas → Parameter errors
2. Ignoring quality metrics → Using unreliable data
3. Wrong tool for task → Check decision trees in rule files
4. Not polling jobs → Missing prediction results

---

Tip: When in doubt, search for tools: GET /api/v1/tools/search?q=your_query