> ## Documentation Index > Fetch the complete documentation index at: https://docs.openbio.tech/llms.txt > Use this file to discover all available pages before exploring further. # Tools Overview > Complete reference of all tools available in OpenBio OpenBio provides access to a comprehensive suite of computational biology tools. This reference documents all available tools and their capabilities. ## Tool Categories OpenBio tools are organized into six main categories: Query biological databases (PDB, UniProt, ChEMBL, PubMed, and more) AI-powered structure prediction and protein design Chemical analysis and molecular property calculations Primer design, PCR, cloning, and molecular biology File management, notebooks, workflows, and more ## 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 ## Tool Capabilities by Domain ### 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, BoltzGen, SimpleFold, PDB search, structure visualization ### 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 ### 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 ### 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 ### 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 ### 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, Reactome, MyVariant, MyTaxon ## 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" ``` ## Using Tools Effectively ### 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 ## Tool Updates OpenBio tools are continuously updated. **Stay informed**: * Check "What's New" in OpenBio * Review changelog for updates * Join our [Discord](https://discord.gg/fd8QbDv9RQ) and X([https://x.com/OpenBioAI](https://x.com/OpenBioAI)) for real-time updates ## Next Steps Explore detailed tool references by category: PDB, UniProt, ChEMBL, PubMed, and more Structure prediction and protein design Chemical analysis and properties Molecular biology tools 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!