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Nanome

nanome.ai

From $4.17/mo Free plan WebWindowsiOSAndroidAPISelf-hosted
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Spec score 8.9 #2 of 29 in 3D Model Viewer Software

What it is

Nanome is a collaborative platform for visualizing molecular structures and supporting drug discovery work. People can review proteins and small molecules together in real time across web and XR workspaces. Its tools cover measurement, selection, molecule building, protein-ligand interaction analysis, docking pose review, molecular dynamics playback, and rendering. MARA, Nanome’s AI copilot, provides more than 300 scientific tools across 26 categories, including docking, structure prediction, cheminformatics, genomics, and materials science. The platform also offers a REST API for each MARA tool, Jupyter integration, and a Claude Code skill and MCP server. The free web tier accepts PDB, SDF, and CIF uploads; its Starter plan includes three workspaces, one project, 50 MARA credits, five recent files, and seven days of chat history. Paid plans start at $4.17/user/mo billed annually. Every new account gets a 14-day Full license trial without a credit card.

Spec sheet

What it does
Nanome is a collaborative molecular visualization and drug-discovery workspace spanning browser, XR headsets and the MARA AI copilot.Read 15 Oct 2026 · nanome.ai
Product
Nanome is a collaborative molecular visualization and drug discovery platform for reviewing protein and small-molecule structures across web, XR headsets, and its MARA AI copilot.Read 29 Sep 2026 · nanome.ai
Deployment
Commercial Enterprise supports private cloud or on-prem deployment, internal database integration, custom or internal LLM and MCP servers, and custom development.Read 29 Sep 2026 · nanome.ai
Trial
Every new account gets a 14-day Full license trial with no credit card required.Read 29 Sep 2026 · nanome.ai
Integrations
Named integrations include Schrödinger LiveDesign, CDD Vault, OpenEye/Cadence, Discngine 3decision, KNIME Server, CCG MOE, Boltz, OpenFold and public scientific databases.Read 15 Oct 2026 · nanome.ai
Support
The pricing page describes premium customer support for Commercial Cloud, and setup assistance and managed devices for Academic Department deployments.Read 29 Sep 2026 · nanome.ai
Headquarters
San Diego, California, United StatesRead 28 Sep 2026 · nanome.ai
Founded
2015Read 28 Sep 2026 · nanome.ai
Academic users
Academic Personal is intended for individual students and researchers, while Academic Department targets institutions and labs deploying at scale and has a 50-license minimum.Read 29 Sep 2026 · nanome.ai
Account security
Nanome account administrators can configure single sign-on and enable two-factor authentication in license management.Read 29 Sep 2026 · nanome.ai
Claude and MCP
Nanome publishes a Claude Code skill and an MCP server for agent-driven workspace creation and scientific tool execution.Read 15 Oct 2026 · nanome.ai
Collaboration
Multiple people can join the same workspace in real time across web and XR.Read 29 Sep 2026 · nanome.ai
Company facts
LinkedIn lists Nanome as a privately held software-development company founded in 2015, headquartered in San Diego, California, with 11–50 employees.Read 15 Oct 2026 · linkedin.com
Documentation
The help center covers setup, hardware, MDM enrollment, networking, installation, account administration, sessions, troubleshooting and legacy plugin development.Read 15 Oct 2026 · help.nanome.ai
Editing tools
The feature set includes amino-acid mutation, rotamer editing, structure minimization, measurement, selection and a 3D chemical builder.Read 15 Oct 2026 · help.nanome.ai
File support
The free web tier allows direct upload of PDB, SDF, and CIF files.Read 29 Sep 2026 · nanome.ai
Independent classroom evidence
A 2025 peer-reviewed teaching study reported that all participating students found Nanome activities somewhat or very helpful and 85% said interest in biomolecular structures increased.Read 15 Oct 2026 · pubmed.ncbi.nlm.nih.gov
Independent review availability
Capterra and Software Advice both displayed no user reviews for Nanome when accessed in October 2026, so repeated praise or complaint themes are not established on those directories.Read 15 Oct 2026 · capterra.com
Interaction analysis
The interaction tools highlight chemical contacts, allow inline annotations and can generate an interaction report.Read 15 Oct 2026 · nanome.ai
Legacy plugin API
Nanome Classic provided a Python-based plugin system and cloud-hosted Stacks for computational integrations.Read 15 Oct 2026 · help.nanome.ai
Limit: feature maturity
Nanome's v2.5 release labels the torsion-angle tool beta and documents known bugs; trajectories above 2,000 frames are not currently supported in the stated cap.Read 15 Oct 2026 · nanome.ai
Limit: headset workflow
The PLOS review says Nanome work is performed inside the VR headset, whereas ChimeraX allows editing in 2D before entering 3D.Read 15 Oct 2026 · yoursay.plos.org
Limit: proprietary licensing
An Oxford review characterizes Nanome as proprietary and says its commercial licensing limits custom extension, with advanced features requiring paid licenses.Read 15 Oct 2026 · academic.oup.com
MARA AI
MARA accepts natural-language requests and runs docking, cheminformatics, structure-preparation and other scientific tools inside a workspace.Read 15 Oct 2026 · nanome.ai
Molecular visualization
Users can load protein and small-molecule structures, build 3D scenes, inspect binding sites and review docking poses.Read 15 Oct 2026 · nanome.ai
Molecule import
Supported sources include RCSB PDB, PubChem, DrugBank and local files, with PDB, SDF and CIF uploads listed for the web plan.Read 15 Oct 2026 · help.nanome.ai
Network requirements
Hosted deployments require outbound TCP 443 to Nanome domains, and the setup guide says TLS/SSL inspection should be exempted for those hosts.Read 15 Oct 2026 · nanome.ai
Notable limits
Starter provides web-based visualization with three workspaces, one project, 50 MARA credits, five most recent files, and seven days of chat history.Read 29 Sep 2026 · nanome.ai
Praise: ease and collaboration
A PLOS contributor called Nanome polished and easy to use, highlighting customizable controls, third-party ligand tools and simultaneous multi-user sessions.Read 15 Oct 2026 · yoursay.plos.org
Praise: usability
A Brown University evaluation described Nanome as among the most user-friendly and technically rigorous molecular-visualization options it examined.Read 15 Oct 2026 · vrwiki.cs.brown.edu
Programmatic access
Nanome provides a REST API for every MARA tool, plus Jupyter integration and a Claude Code skill and MCP server.Read 29 Sep 2026 · nanome.ai
Python and notebooks
A Python package lets users call MARA tools from Jupyter notebooks with an API key.Read 15 Oct 2026 · nanome.ai
Rating on Capterra
0.0 out of 5 from 0 reviews.Read 15 Oct 2026 · capterra.com
Rating on Quest Store DB
3.8 out of 5 from 25 ratings for the Nanome Quest listing.Read 15 Oct 2026 · queststoredb.com
Rating on Software Advice
No rating available because the listing shows no user reviews.Read 15 Oct 2026 · softwareadvice.com
Real-time collaboration
Web, XR and PCVR users can join the same live workspace and see molecular changes together.Read 15 Oct 2026 · nanome.ai
Release news
Version 2.6.1, dated August 14, 2026, added scene recording, a residue editor and in-headset MARA tools alongside fixes.Read 15 Oct 2026 · nanome.ai
REST API
Nanome states that every MARA tool is exposed as a REST endpoint for pipelines, CI/CD and automation.Read 15 Oct 2026 · nanome.ai
Scientific tools
MARA provides a growing library of 300+ scientific tools across 26 categories, including docking, structure prediction, cheminformatics, genomics, and materials science.Read 29 Sep 2026 · nanome.ai
Security controls
The administration site supports SSO, organization membership, license assignment, invoices and two-factor authentication.Read 15 Oct 2026 · nanome.ai
Security limitation
Nanome's terms state that absolute security of electronic transmission cannot be guaranteed.Read 15 Oct 2026 · nanome.ai
Self-hosting
Commercial Enterprise deployments can run in a customer private cloud or on premises behind the firewall, with internal database and LLM/MCP integration.Read 15 Oct 2026 · nanome.ai
Supported devices
The setup page lists Meta Quest 3 and 3S, Samsung Galaxy XR, Apple Vision Pro, Windows PCs over Meta Link, and the browser app without a headset.Read 29 Sep 2026 · nanome.ai
System requirements
Current Nanome v2 supports Meta Quest 3/3S, Samsung Galaxy XR, Apple Vision Pro, Windows PCs over Meta Link and modern browsers; the documented PC minimum GPU is GTX 1070 with RTX 3060 recommended.Read 15 Oct 2026 · help.nanome.ai
Trajectory playback
Nanome can play molecular-dynamics trajectories frame by frame and synchronize playback for collaborators; the current documented cap is 2,000 frames per trajectory.Read 15 Oct 2026 · nanome.ai
Unsupported desktop systems
The help center says Mac and Linux are not currently supported for Nanome desktop use.Read 15 Oct 2026 · help.nanome.ai
Visualization
The platform includes measurement, selection, builder, protein-ligand interaction analysis, docking pose review, molecular dynamics playback, and rendering tools.Read 29 Sep 2026 · nanome.ai

Plans and prices

Starter / Free Web Seat Free 3 workspaces · 1 project · PDB/SDF/CIF upload · view-only XR collaboration · 50 MARA credits · 5 most recent files · 7 days chat history Read 15 Oct 2026 · nanome.ai
Academic Department Full Web Seat $4.17 a month Billed annually; minimum 50 licenses Managed devices · shared molecular storage · syllabus and course implementation assistance Read 15 Oct 2026 · nanome.ai
Academic Department Full seat $12.50 a month Billed annually MCP calls: Custom · Minimum 50 licenses Read 29 Sep 2026 · nanome.ai
Academic Department Full Seat $12.50 a month Billed annually; minimum 50 licenses Web and XR · managed devices · shared molecular storage · implementation assistance Read 15 Oct 2026 · nanome.ai
Academic Classroom / Personal Full Seat $20.83 a month Billed annually Web plus XR · shared Nanome collaboration server · 300+ tools · 100 MCP calls · custom hosted tools Read 15 Oct 2026 · nanome.ai
Academic Personal Full seat $20.83 a month Billed annually 100 MCP calls · Nanome-hosted shared tenant collaboration server · 300+ tools Read 29 Sep 2026 · nanome.ai
Commercial Cloud / Enterprise Priced on request Custom MCP calls · Cloud or Enterprise deployment · Premium support Read 29 Sep 2026 · nanome.ai
Commercial Cloud or Enterprise Priced on request Single-tenant cloud or behind-firewall deployment · 300+ tools · custom tools · internal database and LLM/MCP integration · dedicated IT support Read 15 Oct 2026 · nanome.ai

Every Nanome plan and price →

Strong points and limits

Strong points

  • Real-time collaboration across web and XR.
  • MARA includes 300+ tools across 26 categories.
  • REST API access for every MARA tool.
  • Free web tier accepts PDB, SDF, and CIF uploads.

Limits

  • Starter is limited to three workspaces and one project.
  • Starter includes 50 MARA credits.
  • Academic Department plans require at least 50 licenses.

Who it suits

Nanome suits researchers and teams reviewing molecular structures together, including users working across web and supported XR devices. Academic users can choose individual or department plans; Commercial Enterprise supports private cloud or on-prem deployment.

Nanome in depth

Read the full write-up

Overview

Nanome is a collaborative molecular-visualization and drug-discovery platform for protein and small-molecule work in the browser and supported XR headsets. It suits researchers and labs that need to review structures together or connect them to scientific tools and code. The breadth is compelling, but Starter’s tight caps and the 50-license academic department minimum make plan choice important.

Key features

Nanome covers more than viewing: users can measure and select structures, build molecules, analyze protein–ligand interactions, review docking poses, play back molecular dynamics and render scenes. That combination suits active structure review, rather than readers who only need a basic model viewer. The free web tier accepts direct PDB, SDF and CIF uploads; broader supported formats include mmCIF/PDBx, MOL, MOL2, SMILES, XYZ, PQR, PDBQT, MAE, MAEGZ, MOE, PSE, GRO, XTC, TRR, DCD and DX.

People can join the same workspace in real time across web and XR, which makes shared review a core strength. Integrations include Schrödinger LiveDesign, CDD Vault, OpenEye/Cadence, Discngine 3decision, KNIME Server, CCG MOE, Boltz and OpenFold. MARA adds a library of 300+ scientific tools across 26 categories, including docking, structure prediction, cheminformatics, genomics and materials science. Each MARA tool has a REST API; Jupyter integration, a Claude Code skill and an MCP server give technical teams additional ways to connect tools to workflows.

Commercial Enterprise supports private-cloud or on-prem deployment, internal database integration, custom or internal LLM and MCP servers, and custom development. Administrators can configure single sign-on and enable two-factor authentication in license management. These options suit organizations with deployment or account-security requirements, but come with custom pricing rather than a published entry price.

Pricing

Nanome uses a freemium model, with a 14-day Full license trial for every new account and no credit card required. Starter / Free Web Seat costs nothing. It includes web visualization, three workspaces, one project, 50 MARA credits, the five most recent files and seven days of chat history. Those limits make it useful for trying the workflow or occasional review, but restrictive for ongoing work with multiple projects or a larger file history.

Academic Department Full Web Seat costs $4.17 a month, billed annually, starting at a minimum of 50 licenses. The Academic Department Full seat costs $12.50 a month, also billed annually, with custom MCP calls and the same 50-license minimum. Department deployments also include setup assistance and managed devices. The lower-priced web seat is the more economical department option; the higher tier is relevant when custom MCP calls matter. Either minimum makes these plans a poor fit for a single academic user.

Academic Personal Full seat costs $20.83 a month, billed annually. It includes 100 MCP calls, a Nanome-hosted shared tenant collaboration server and 300+ tools, making it the clearest paid fit for an individual student or researcher seeking the broader toolset. Commercial Cloud / Enterprise has custom pricing, custom MCP calls, cloud or enterprise deployment and premium support. Nanome does not publish a single price for that organizational tier.

Platforms

Nanome supports web, Windows and Android XR, along with supported XR headsets. The setup page names Meta Quest 3 and 3S, Samsung Galaxy XR, Apple Vision Pro and Windows PCs over Meta Link; the browser app also works without a headset. The platform mix lets teams combine browser-based access with immersive review, while the XR device choices are specific rather than universal.

Who it's for

Nanome is best suited to molecular researchers, students and lab teams who need collaborative structure review, scientific analysis or programmatic access. Academic Personal is aimed at individual students and researchers; the department plans target labs and institutions deploying at scale. It is less suitable for someone who only needs to view generic 3D models, or for a small lab that cannot meet the department plan’s 50-license floor.

Pros and cons

Pro: Measurement, interaction analysis, docking review and molecular-dynamics playback put useful scientific review tools alongside visualization.

Pro: Real-time collaboration spans web and XR, and the supported formats cover a wide range of molecular and simulation files.

Pro: MARA’s 300+ tools, REST APIs and Jupyter integration provide substantial scope for extending scientific workflows.

Con: Starter allows only three workspaces, one project, 50 credits, five recent files and seven days of chat history, limiting sustained free use.

Con: Academic Department pricing requires at least 50 licenses, so it is not a practical route for a small team.

Con: Commercial Enterprise uses custom pricing, making its cost harder to compare before contacting Nanome.

Alternatives

For a more general 3D-viewing need, 3D Model Viewer Software and 3D Visualization Software are broader starting points. Choose Dalux instead if a free punch-list tool with unlimited tasks and up to three active projects or buildings is a better fit. Sketchfab suits general model sharing across more operating systems; its free Basic plan caps each model at 50 MB, while Pro is $15 a month billed yearly.

Aspose.3D Viewer is a free option for readers who want a general viewer rather than Nanome’s molecular workflow. BIMcollab is the alternative to consider for BIM collaboration; its Basic annual plan is €12.50 a month and includes 10 GB storage per space and one guest access. OmniView 3D offers a free Starter plan for up to three models and 100 MB storage, with automatic deletion after three days and a watermark; pick it when those general model-sharing limits are acceptable.

BIMx Web Viewer provides free browser viewing for readers working with BIMx models. Marmoset Viewer is included with Toolbag versions 2.07 and newer. F3D is the free, open-source alternative under the BSD 3-Clause License.

Verdict

Choose Nanome if your work centers on molecular structures and you need collaborative review backed by scientific tools, integrations or programmatic access. Its combination of real-time web and XR workspaces with MARA is the principal reason to prefer it over a general 3D viewer. Look elsewhere if Starter’s caps are too restrictive, your academic group cannot buy 50 licenses, or you need a published Enterprise price before evaluating deployment.

Verdict

Nanome brings collaborative structure visualization together with scientific tools and programmatic access. Check Starter’s workspace, project, credit, file, and chat-history limits against your needs, and note that academic department pricing starts at a 50-license minimum.

Where Specifiction places it

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