# Ivy Biosciences Docs

> Auto-generated index of the Ivy Biosciences documentation, mirroring the docs sidebar. Grouped by section, in reading order. Append `.md` or send `Accept: text/markdown` to any docs URL for its raw markdown.

## Start here


## Get started

- [Overview](https://www.ivybiosciences.com/docs/overview): How the platform fits together in 90 seconds — one request becomes tools, jobs, and interactive results on the canvas.
- [Getting Started](https://www.ivybiosciences.com/docs/getting-started): Create your account, understand subscription tiers, and choose the right workspace for your drug discovery workflow.
- [Plans and tiers](https://www.ivybiosciences.com/docs/plans-and-tiers): How the platform meters usage with credits and gates capability by plan — the active subscription tiers and what each one unlocks.
- [Which tool?](https://www.ivybiosciences.com/docs/which-tool): Match a scientific goal to the tool or workflow that answers it — grouped by stage of the discovery pipeline.
- [What you can achieve](https://www.ivybiosciences.com/docs/capabilities): Start from the outcome, not the tool. Most goals are served by more than one tool that does roughly the same thing — here's the capability and which tool fits.
- [Concept clusters](https://www.ivybiosciences.com/docs/concept-clusters): Every platform concept, grouped into five clusters. Each cluster answers one question about how work moves through the platform.
- [Decisions](https://www.ivybiosciences.com/docs/decisions): Close-cousin concepts, side by side — pick the right surface, work unit, and organizational container for the task in front of you.
- [Glossary](https://www.ivybiosciences.com/docs/glossary): Every platform term in one place — grouped by concept cluster, then listed A–Z for lookup.

## Entry points

- [Chat Workspace](https://www.ivybiosciences.com/docs/chat): The conversational surface for drug discovery — describe a goal in plain language and the orchestrator selects tools, chains steps, and renders results.
- [Studio Workspace](https://www.ivybiosciences.com/docs/studio): The project-based surface — a file explorer, job dashboard, canvas, and floating windows for direct control over files, parameters, and layout.
- [IvyBloom CLI Documentation](https://www.ivybiosciences.com/docs/cli): Command-line interface for running protein folding, molecular docking, and analysis from your terminal.
- [MCP server](https://www.ivybiosciences.com/docs/mcp): Expose the platform to AI agents as callable tools over the Model Context Protocol.
- [API Documentation](https://www.ivybiosciences.com/docs/api): Complete API reference for Ivy Biosciences — REST API, Harness Sessions, TypeScript SDK, real-time protocols, and interactive reference

## How it works

- [How the orchestrator picks tools](https://www.ivybiosciences.com/docs/how-orchestration-works): You describe a goal in plain language; the orchestrator maps it to tools and chains them. Here is what happens between your message and the results, and how to steer it.
- [How tools run](https://www.ivybiosciences.com/docs/how-tools-run): Every tool executes one of a few ways — on a GPU as a tracked job, as an instant lookup, in your sandbox, or over the results you already have. How a tool runs decides its latency, cost, and where its output lands.
- [What a passport is](https://www.ivybiosciences.com/docs/passports-explained): A passport aggregates several tools into one profile. Here is the model behind it, how it differs from running tools yourself, and when to reach for one.

## Use cases & recipes

- [Recipes](https://www.ivybiosciences.com/docs/recipes): Copy-and-adapt tool chains for common discovery goals. Each recipe is one prompt, the pipeline it triggers, and the gotchas to watch.
- [Antibody engineering](https://www.ivybiosciences.com/docs/antibodies): Number, humanize, profile developability, and mine repertoires for therapeutic antibodies and AAV gene-therapy vectors on the platform.
- [Structure Prediction overview](https://www.ivybiosciences.com/docs/structure-prediction): Predict or fetch a protein's 3D structure and analyze it.
- [Docking & MD overview](https://www.ivybiosciences.com/docs/docking): Find pockets, dock small molecules, and rescore by binding energy.
- [ADMET overview](https://www.ivybiosciences.com/docs/admet): Predict pharmacokinetics, safety, and solubility for compounds.
- [Generative & De Novo overview](https://www.ivybiosciences.com/docs/generative): Generate novel molecules or grow fragments toward a target profile.
- [Cheminformatics overview](https://www.ivybiosciences.com/docs/cheminformatics): Turn SMILES into descriptors, standardize structures, classify reactions.
- [Genomics & Multi-Omics overview](https://www.ivybiosciences.com/docs/genomics-omics): Analyze bulk and single-cell omics to nominate druggable targets.
- [Cell & Tissue overview](https://www.ivybiosciences.com/docs/cell-tissue): Cell-therapy design, cytometry, and pathology analysis.
- [Targets & Modalities overview](https://www.ivybiosciences.com/docs/targets-modalities): Specialized target classes and drug modalities.
- [Materials & Crystals overview](https://www.ivybiosciences.com/docs/materials-crystals): Predict crystal polymorphs and simulate diffraction patterns.
- [Databases overview](https://www.ivybiosciences.com/docs/databases): Search curated chemical, biological, clinical, and literature databases.
- [Predictors overview](https://www.ivybiosciences.com/docs/predictors): Specialized property and safety predictors.
- [Lab Operations overview](https://www.ivybiosciences.com/docs/lab-operations): Lab automation and local data processing.
- [Passports & Reports](https://www.ivybiosciences.com/docs/passports): Multi-source aggregated reports that compile data from multiple tools into comprehensive profiles.
- [Workflows](https://www.ivybiosciences.com/docs/workflows): End-to-end drug discovery workflows that chain multiple tools into guided pipelines.
- [Smart Workflows](https://www.ivybiosciences.com/docs/smart): Multi-tool orchestrated pipelines that chain tools automatically with a single request.

## Modal GPU tools

- [Modal GPU tools](https://www.ivybiosciences.com/docs/modal-gpu-tools): The heavy scientific compute — folding, docking, ADMET, generative design, omics, and more — that runs as tracked GPU jobs, produces artifacts, and consumes credits.
- [ESMFold on the platform](https://www.ivybiosciences.com/docs/esmfold): Predict protein structures with ESMFold and interpret confidence metrics.
- [AlphaFold on the platform](https://www.ivybiosciences.com/docs/alphafold): Fetch pre-computed AlphaFold structures from the EBI AlphaFold Database by UniProt ID.
- [ESM-3 on the platform](https://www.ivybiosciences.com/docs/esm3): Protein language model embeddings and functional analysis with ESM-3.
- [PDB2PQR](https://www.ivybiosciences.com/docs/pdb2pqr): Assign protonation states and prepare proteins for electrostatics calculations.
- [BLAST](https://www.ivybiosciences.com/docs/blast): Run NCBI BLAST locally or remotely from platform jobs.
- [DiffDock on the platform](https://www.ivybiosciences.com/docs/diffdock): Run diffusion-based protein–ligand docking with reproducible settings.
- [MM-GBSA](https://www.ivybiosciences.com/docs/mmgbsa): Calculate binding free energies with GPU-accelerated MM-GBSA using OpenMM.
- [P2Rank](https://www.ivybiosciences.com/docs/p2rank): Predict protein binding sites with ML-based pocket detection and druggability scoring.
- [ADMET-AI](https://www.ivybiosciences.com/docs/admet_ai): Use ADMET-AI inside the platform to predict ADMET risk early.
- [ADMETlab 3.0](https://www.ivybiosciences.com/docs/admetlab3): Use ADMETlab 3.0 inside the platform for multi-endpoint ADMET profiling.
- [DeepChem on the platform](https://www.ivybiosciences.com/docs/deepchem): Molecular machine learning for property prediction and drug discovery.
- [DeepPurpose](https://www.ivybiosciences.com/docs/deeppurpose): Train and run DeepPurpose models for drug-target prediction on the platform.
- [DeepSol on the platform](https://www.ivybiosciences.com/docs/deepsol): Run aqueous solubility predictions for small molecules.
- [GraphSol](https://www.ivybiosciences.com/docs/graphsol): Predict protein solubility from amino acid sequences with GraphSol.
- [REINVENT](https://www.ivybiosciences.com/docs/reinvent): Configure de novo design runs with REINVENT on the platform.
- [GenMol](https://www.ivybiosciences.com/docs/genmol): Generate novel molecules using masked discrete diffusion on SAFE representations.
- [Fragment Growing](https://www.ivybiosciences.com/docs/fragment_growing): Grow seed fragments into tractable analog series with quality controls.
- [Fragment Library](https://www.ivybiosciences.com/docs/fragment_library): Search curated fragment collections with property, substructure, and similarity filters.
- [AiZynthFinder](https://www.ivybiosciences.com/docs/aizynthfinder): Plan retrosynthesis routes with AiZynthFinder inside the platform.
- [RDKit Toolkit](https://www.ivybiosciences.com/docs/rdkit): Practical guide to run cheminformatics workflows with RDKit.
- [RXNFP](https://www.ivybiosciences.com/docs/rxnfp): Generate reaction fingerprints and run similarity searches with RXNBERT transformer models.
- [Reaction Classifier](https://www.ivybiosciences.com/docs/reaction_classifier): Classify chemical reactions and suggest conditions using Rxn-INSIGHT with RXNFP fallback.
- [Genomics on the platform](https://www.ivybiosciences.com/docs/genomics): Multi-database genomics query tools for gene information, pathway analysis, variant interpretation, and cross-database linking.
- [Epigenomics on the platform](https://www.ivybiosciences.com/docs/epigenomics): Chromatin accessibility, histone modification, and DNA methylation analysis tools for epigenomic profiling.
- [Metagenomics on the platform](https://www.ivybiosciences.com/docs/metagenomics): Taxonomic classification, community profiling, diversity analysis, and differential abundance tools for microbiome and metagenomic studies.
- [Causal Genomics on the platform](https://www.ivybiosciences.com/docs/causal_genomics): Statistical genetics tools for Mendelian randomization, fine-mapping, colocalization, and LD score regression to identify causal variants and estimate heritability.
- [Scanpy on the platform](https://www.ivybiosciences.com/docs/scanpy): Single-cell RNA-seq analysis with Scanpy for preprocessing, clustering, and trajectory inference.
- [scvi-tools on the platform](https://www.ivybiosciences.com/docs/scvi_tools): Deep generative models for single-cell RNA-seq analysis including batch correction, cell type annotation, doublet detection, and multi-modal integration.
- [Spatial Omics on the platform](https://www.ivybiosciences.com/docs/spatial_omics): Spatial transcriptomics tools for cell deconvolution, cell-cell communication analysis, and spatial domain identification from tissue sections.
- [Proteomics on the platform](https://www.ivybiosciences.com/docs/proteomics): Search PRIDE mass spectrometry datasets and EMDB cryo-EM structures for protein identification, quantification, and structural analysis.
- [Metabolomics on the platform](https://www.ivybiosciences.com/docs/metabolomics): Metabolomics data preprocessing, metabolite annotation, differential analysis, and pathway enrichment tools for mass spectrometry workflows.
- [Transformers on the platform](https://www.ivybiosciences.com/docs/transformers): Biomedical NLP and entity extraction with Hugging Face transformer models.
- [Cell & Gene Therapy on the platform](https://www.ivybiosciences.com/docs/cell_therapy): Computational tools for CAR-T design, CAR construct assembly, safety prediction, manufacturing scoring, NK-CAR design, KIR matching, and cytotoxicity prediction.
- [Cytometry on the platform](https://www.ivybiosciences.com/docs/cytometry): Automated gating, unsupervised clustering, differential population analysis, and imaging mass cytometry tools for flow, mass, and imaging cytometry data.
- [Pathology on the platform](https://www.ivybiosciences.com/docs/pathology): Digital pathology analysis for whole slide images — tiling, tissue detection, and deep-learning feature extraction.
- [frogs](https://www.ivybiosciences.com/docs/frogs): Analyze compound-target annotations and gene signatures to connect molecules with pathway activity.
- [CRISPR on the platform](https://www.ivybiosciences.com/docs/crispr): Guide RNA design, off-target analysis, and CRISPR screen hit identification for genome editing experiments.
- [PROTAC design on the platform](https://www.ivybiosciences.com/docs/protac): Targeted protein degradation tools for PROTAC linker enumeration, ternary complex modeling, and degradation efficiency prediction.
- [Oncology Analytics on the platform](https://www.ivybiosciences.com/docs/oncology): Computational oncology tools for HRD scoring, tumor mutational burden, liquid biopsy analysis, and immunotherapy biomarker prediction.
- [Systems Biology on the platform](https://www.ivybiosciences.com/docs/systems_biology): Flux balance analysis, metabolic model construction, and gene essentiality prediction tools for genome-scale metabolic modeling.
- [OpXRD](https://www.ivybiosciences.com/docs/opxrd): Search and analyze X-ray powder diffraction patterns from the opXRD database.
- [XTalNet](https://www.ivybiosciences.com/docs/xtalnet): Run crystal-structure modeling and refinement pipelines with XTalNet.
- [PyWPEM](https://www.ivybiosciences.com/docs/pywpem): GPU-powered X-ray diffraction refinement, simulation, and spectroscopy analysis.
- [BioBERT](https://www.ivybiosciences.com/docs/biobert): Use BioBERT for biomedical text mining and NLP on the platform.
- [ProTox-3](https://www.ivybiosciences.com/docs/protox3): Use ProTox-3 inside the platform for comprehensive toxicity prediction.
- [validation monitor on the platform](https://www.ivybiosciences.com/docs/validation_monitor): Validate computational predictions against experimental results and track hit validation with a test-suite report.
- [Bayesian Optimization on the platform](https://www.ivybiosciences.com/docs/bayesian): Probabilistic multi-parameter optimization for lead compound design using Gaussian processes.
- [ANARCI on the platform](https://www.ivybiosciences.com/docs/anarci): Number antibody sequences to canonical schemes and annotate CDRs, framework regions, and germline genes with ANARCI.
- [IgBLAST on the platform](https://www.ivybiosciences.com/docs/igblast): Assign V(D)J germline genes, annotate CDRs, and measure somatic hypermutation for antibody sequences with IgBLAST.
- [OAS search on the platform](https://www.ivybiosciences.com/docs/oas_search): Search the Observed Antibody Space — billions of natural antibody sequences — for homologs of your candidate with KA-Search.
- [Humatch on the platform](https://www.ivybiosciences.com/docs/humatch): Score antibody humanness against the human germline repertoire with a deep-learning classifier, per V-gene and per position.
- [BioPhi on the platform](https://www.ivybiosciences.com/docs/biophi): Score antibody humanness with OASis and humanize sequences with the Sapiens deep-learning model or CDR grafting using BioPhi.
- [Paragraph on the platform](https://www.ivybiosciences.com/docs/paragraph): Predict which antibody residues contact the antigen — the paratope — with a graph neural network, using Paragraph.
- [Antibody developability on the platform](https://www.ivybiosciences.com/docs/antibody_developability): Profile whether an antibody can be manufactured — TAP, charge, pI, aggregation, viscosity, and sequence liabilities — in one assessment.
- [AAV design on the platform](https://www.ivybiosciences.com/docs/aav): Select an AAV capsid serotype for a target tissue and optimize the transgene cassette for AAV packaging — the gene-therapy tools of the biologics cluster.

## Database & lookup tools

- [Database & lookup tools](https://www.ivybiosciences.com/docs/database-lookup-tools): Instant, inline lookups against external databases — compounds, targets, literature, and trials — that return directly in the canvas with no job to track.
- [ChEMBL on the platform](https://www.ivybiosciences.com/docs/chembl): Search Europe's largest open bioactivity database for compounds, targets, and assay data.
- [PubChem search](https://www.ivybiosciences.com/docs/pubchem): Query PubChem, filter results, and export data through the platform.
- [PubMed Search on the platform](https://www.ivybiosciences.com/docs/pubmed): Search PubMed/MEDLINE for biomedical literature using natural language or Boolean queries.
- [UniProt Search on the platform](https://www.ivybiosciences.com/docs/uniprot): Search the UniProt protein database for sequences, annotations, GO terms, and cross-references.
- [PDB Search & Download on the platform](https://www.ivybiosciences.com/docs/pdb): Search and retrieve protein structures from the RCSB Protein Data Bank.
- [Biotite](https://www.ivybiosciences.com/docs/biotite): Python toolkit for sequence and structure bioinformatics on the platform.
- [Molport sourcing](https://www.ivybiosciences.com/docs/molport): Search suppliers and manage sourcing lists with Molport in the platform.
- [ZINC Database](https://www.ivybiosciences.com/docs/zinc): Query, filter, and download ZINC compounds through the platform workflows.
- [Clinical Trials Search on the platform](https://www.ivybiosciences.com/docs/clinical_trials): Search ClinicalTrials.gov for active and completed trials by condition, intervention, phase, and status.

## Galaxy bridge tools

- [The Galaxy bridge](https://www.ivybiosciences.com/docs/galaxy): A bridge to a hosted Galaxy bioinformatics server that adds dozens of sequencing and genomics tools as an HTTP-async execution class, distinct from the Modal GPU jobs.

## Lab & local tools

- [Lab & local tools](https://www.ivybiosciences.com/docs/lab-local-tools): Bench-automation bridges and client-side processing utilities — protocol generation for lab robots, data transforms, and on-device steps.
- [Lab Automation on the platform](https://www.ivybiosciences.com/docs/lab_automation): Automated liquid handling protocol generation and robotic lab experiment submission for Opentrons and Adaptyv Bio.
- [Data Processing on the platform](https://www.ivybiosciences.com/docs/data_processing): ETL pipelines for transforming, aggregating, converting, and validating tabular datasets.
- [Local Processing](https://www.ivybiosciences.com/docs/local_processing): Client-side data processing for format conversion, fingerprints, and cheminformatics.
- [AI Analysis Local](https://www.ivybiosciences.com/docs/ai_analysis_local): Client-side AI-powered molecular data analysis with local LLM inference.

## Sandbox tools

- [The workspace sandbox](https://www.ivybiosciences.com/docs/sandbox): A per-chat Linux compute environment where the platform runs code, inspects files, and post-processes tool results.

## Meta & data tools

- [Meta and data tools](https://www.ivybiosciences.com/docs/meta-tools): The execution class that operates on the session's prior results and orchestration — retrieving offloaded data, no new compute, no job record.

## Operate

- [Troubleshooting](https://www.ivybiosciences.com/docs/troubleshooting): Start here when something breaks — a symptom-to-page router across login, network, jobs, uploads, billing, and the workspaces.
- [Next Steps](https://www.ivybiosciences.com/docs/nextsteps): What to do once you've exported results — verify outputs, hand off to external tools, and translate in-silico predictions into wet lab experiments.