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OpenBio provides access to a comprehensive suite of computational biology tools. This reference documents all available tools and their capabilities.

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Tool Categories

OpenBio tools are organized into six main categories:

Database Tools

Query biological databases (PDB, UniProt, ChEMBL, PubMed, and more)

Prediction Tools

AI-powered structure prediction and protein design

Molecular Chemistry

Chemical analysis and molecular property calculations

DNA & Biology Tools

Primer design, PCR, cloning, and molecular biology

Utilities

File management, notebooks, workflows, and more

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How Tools Work

When you chat with OpenBio, it will automatically:
  1. Understands your intent from natural language
  2. Selects appropriate tools for the task
  3. Executes tools with correct parameters
  4. Formats results in human-readable form

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Tool Capabilities by Domain

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Structural Biology

What you can do:
  • Predict protein structures from sequences
  • Visualize 3D structures
  • Analyze binding sites and interfaces
Available tools: Boltz-2, Chai-1, SimpleFold, PDB search, structure visualization

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Molecular Design

What you can do:
  • Design protein sequences from structures
  • Create thermostable variants
  • Design protein binders
  • Generate primers and cloning strategies
  • Plan DNA assembly
Available tools: ProteinMPNN, LigandMPNN, ThermoMPNN, Pinal, primer design, Gibson/Golden Gate assembly

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Chemical Biology

What you can do:
  • Search compound databases
  • Calculate molecular properties
  • Analyze chemical structures
  • Assess drug-likeness
  • Predict synthetic accessibility
Available tools: ChEMBL, PubChem, RDKit, SA Score calculator

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Sequence Analysis

What you can do:
  • Analyze protein and DNA sequences
  • Find motifs and domains
  • Search sequence databases
  • Extract sequence features
Available tools: UniProt search, sequence analysis

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Literature Research

What you can do:
  • Search scientific literature
  • Find papers by topic, author, or journal
  • Generate bibliographies
  • Summarize findings
  • Track citations
Available tools: PubMed, ArXiv, BioRxiv, literature analysis

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Genomics & Genetics

What you can do:
  • Look up gene information
  • Find disease associations
  • Analyze genetic variants
  • Search taxonomic data
  • Cross-reference databases
Available tools: MyGene, MyDisease, MyVariant, MyTaxon

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Automatic Parameter Selection

OpenBio fills in sensible defaults: 
You say: "Find kinase structures"
AI selects:
- Database: PDB
- Query: kinase
- Filters: Default (all organisms, all methods)
- Limit: Top 50 results
You can override defaults: 
"Find human kinase structures solved by X-ray with resolution < 2Å"

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Using Tools Effectively

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Best Practices

More details = Better results:
  • Specify organism
  • Include constraints
  • Define desired output format
Refine progressively:
  1. Start with broad query
  2. Review results
  3. Add filters
  4. Narrow to best candidates
Always verify critical results:
  • Cross-reference multiple sources
  • Check primary literature
  • Validate experimentally when possible
Keep notes about:
  • Tools used
  • Parameters chosen
  • Results obtained
  • Next steps

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Tool Updates

OpenBio tools are continuously updated. Stay informed:

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Next Steps

Explore detailed tool references by category:

Database Tools

PDB, UniProt, ChEMBL, PubMed, and more

Prediction Tools

Structure prediction and protein design

Molecular Chemistry

Chemical analysis and properties

DNA & Biology

Molecular biology tools

Utilities

File management and workflows
Pro Tip: You don’t need to memorize tool names. Just describe your goal naturally, and OpenBio will select the right tools automatically!