Your tools. Your data. One interface.

Nanome connects to the scientific software and databases your team already uses. MARA orchestrates them in plain English. Nanome XR puts the results in three dimensions. And Claude Code can drive the whole thing through our MCP server and skill.

Compatible with the platforms your team already relies on

Schrödinger LiveDesign

Pull Live Reports into XR. Iterate on molecular designs spatially.

CDD Vault

Query saved searches and find similar molecules by SMILES.

OpenEye / Cadence

FastROCS shape search, MD trajectory parsing, cryptic pocket evaluation

Discngine 3decision

Browse and retrieve structures from 3decision projects.

KNIME Server

Trigger KNIME workflows, check job status, analyze results

CCG MOE

Import MOE session files directly into Nanome.

Boltz

Biomolecular structure prediction and analysis

OpenFold

Open-source protein structure prediction workflows

Public databases and open-source tools

RCSB PDB AlphaFold DB ChEMBL UniProt UniChem Materials Project AutoDock Vina DiffDock ESMFold OpenFold Consortium Member

0+ scientific tools. One conversation.

MARA ships with a growing library of built-in tools across 26 categories. Docking, structure prediction, cheminformatics, genomics, materials science, and more. Run them in plain English or chain them into multi-step workflows.

Download PDB from RCSBDownload Ligand SDFs from RCSBConvert mmCIF to PDBConvert PDB to PDBQTExtract Protein from StructurePDB File FixerMultiple Sequence AlignmentProtein Sequence Alignment from FASTADraw 2D Molecule from SMILESDraw 2D Molecule from SMARTSCalculate Chemical DescriptorsExtract Functional GroupsR-Group AttachmentParse Core and R-Group PositionsTanimoto Similarity (SMILES)Check Enantiomers3D Conformer GeneratorGenerate Conformers from SDFRun Smina DockingSmina Docking (No Sanitize)Fold Sequence with ESMFoldBoltz Two Proteins YAMLGet MD Trajectory InfoPairwise Distance from TrajectoryFind Pockets with P2RankFind Pockets (Multi-Model)Compute Non-Covalent InteractionsSingle Ligand Interaction MapCreate MMPDB from CSVPredict Property Difference via MMPDBDrug-Likeness FiltersInspect CSV FileQuery CSV with Natural LanguageScatter Plot (2D/3D)HistogramGet ChEMBL ID from UniChem IDPredicted Target InteractionsCreate WorkspaceDelete WorkspaceDownload from Materials ProjectRun APBSWrite Multivalue InputProtein to DNA BacktranslatorReverse Translate with Codon TableRefresh 3decision TokenGet CDD Vault Saved SearchCombine Files to JSONCombine PDBQT and SDF
Get Structure from RCSBDownload SDF by EBI Ligand IDConvert PDB to mmCIFConvert Mol2 to SDF and PDBSave Protein-Only PDBClean Up PDBPairwise Sequence AlignerAnalyze Aligned Sequence DifferencesDraw 2D Molecule from SDFDraw Molecule from UniChem IDGet Properties from ChEMBLIdentify Aromatic Ring AtomsEnumerate Substituent SwapsDecompose Ligand CoreTanimoto Similarity (SDF)Maximum Common SubstructureGenerate Conformers from SMILESGenerate Constrained ConformersSmina Multi-Ligand DockingAlign SDF to PDB LigandBoltz Single Protein YAMLBoltz Docking YAMLCalculate RMSD from TrajectoryAverage Trajectory and Color by RMSDFind Pockets with PocketeerSplit Pockets PDB by ChainLigand Interaction Diagram (PandaMap)2D Protein-Ligand Interaction MapGenerate Molecules from MMPDBDetect Activity CliffsRun Molecular FiltersFilter CSV DataExport Data to CSVBoxplotGet ChEMBL ID from Drug NameSearch ChEMBL by NameList WorkspacesEdit WorkspaceSearch Materials ProjectDFTB+ CalculatorRun MultivalueDraw Plasmid MapReverse Translate AA to DNAList 3decision ProjectsRetrieve Files from 3decisionGet Similar CDD Vault MoleculesCombine Single-Chain PDBsCombine Protein and Ligands
AI-powered molecular analysis

Build custom tools. Wire in your own infrastructure.

Python Snippets

Drop in a snippet, MARA spins up the sandbox. Use AI to write the snippet if you want.

HTTP Endpoints

Point MARA at any REST API and it becomes a conversational tool.

SQL Queries

Query your databases through MARA. Results flow into the rest of your analysis.

Enterprise teams have built integrations with proprietary scoring functions, internal databases, and custom analysis pipelines. Whatever you build is instantly available across your org. Learn how to create tools →

Programmatic access. AI-native workflows.

Jupyter notebook integration

Call MARA from Jupyter. Install the Python package, drop in your API key, and run any MARA tool from the same notebook you're already using.

Learn more →

Claude Code skill and MCP server

Nanome publishes a Claude Code skill and an MCP server. Coding agents can prep config files, run docking, parse results, and reach the full MARA tool library directly.

Learn more →

REST API

Every MARA tool is a REST endpoint. Drop Nanome's capabilities into your own pipelines, CI/CD, and automation infrastructure.

Explore documentation →

All of this, from inside XR.

Every integration, every tool, every workflow is reachable from inside Nanome XR. Run docking, query databases, fire off workflows, walk through the results spatially, all without taking the headset off. MARA voice commands let you do it hands-free.

See what Nanome does with your stack.

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