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Research · head to head

Obsidian vs OpenEye, Cadence Molecular Sciences

Obsidian logo

Obsidian

Research

A powerful knowledge base on top of a local folder of plain text Markdown files

From
Free
Rated
-
Full reviewWebsite
OpenEye, Cadence Molecular Sciences logo

OpenEye, Cadence Molecular Sciences

Research

Computational chemistry toolkits and the Orion cloud platform, now inside Cadence

From
On request
Rated
-
Full reviewWebsite

The short version

  • Only Obsidian has a free tier, so it costs nothing to try first.
  • Each has a real cost: Obsidian sync is a paid add-on at $4 per month billed annually rather than part of the app; OpenEye, Cadence Molecular Sciences the free Public Domain Research Licence requires surrendering intellectual property rights and publishing results into the public domain, which rules it out for any academic group with a technology transfer office or patent ambitions.
  • They diverge on capability: Obsidian covers Bidirectional linking, OpenEye, Cadence Molecular Sciences covers OMEGA.
  • Prices and features above were last checked on 31 August 2026.

Where they differ

Only the attributes on which Obsidian and OpenEye, Cadence Molecular Sciences actually diverge.

Attributes where Obsidian and OpenEye, Cadence Molecular Sciences differ
AttributeObsidianOpenEye, Cadence Molecular Sciences
Starting priceFreeOn request
Pricing modelUnknownquote
Free tierYesNo
PlatformsWeb, Windows, macOS, Linux, iOS, AndroidLinux, Windows, macOS, Web, API
Founded2020Unknown

Identical on both: user rating (Not yet rated), category (Research).

What each one covers

Drawn from each product's published feature list. An absence here means we hold no record of it - not that the product lacks it.

Only in Obsidian

  • Bidirectional linking
  • Graph view visualization
  • Markdown support
  • Local file storage
  • Plugin ecosystem
  • Custom CSS themes
  • Templates
  • Search and tags

Only in OpenEye, Cadence Molecular Sciences

  • OMEGA
  • ROCS
  • ROCS X
  • Orion platform
  • Programmatic toolkits
  • Academic routes
  • Structure preparation
  • Docking and scoring

What people use each for

The jobs each tool is most often brought in to do.

Obsidian

  • Local-first markdown note taking with no account requirednot OpenEye, Cadence Molecular Sciences
  • Linking notes into a personal knowledge graphnot OpenEye, Cadence Molecular Sciences
  • Syncing a vault across devices with end-to-end encryption on the paid add-onnot OpenEye, Cadence Molecular Sciences
  • Publishing a public site from a vaultnot OpenEye, Cadence Molecular Sciences
  • Extending the editor with community pluginsnot OpenEye, Cadence Molecular Sciences

OpenEye, Cadence Molecular Sciences

  • A pharmaceutical discovery team screening a multi-billion compound library by three-dimensional shape rather than by two-dimensional similaritynot Obsidian
  • A computational chemist embedding conformer generation into an internal pipeline through the Python toolkitsnot Obsidian
  • A university group publishing openly that can accept the public domain licence terms in exchange for zero costnot Obsidian
  • A biotech scaling virtual screening on cloud compute without building its own clusternot Obsidian

Where each one falls short

Documented limitations, not opinions. Every one is a constraint you would hit in normal use.

Obsidian

  • Sync is a paid add-on at $4 per month billed annually rather than part of the app
  • Publishing to the web is a further $8 per month per site
  • Commercial use asks for a $50 per user per year licence, though the vendor states it is not required
  • Collaboration is limited compared with a hosted notes tool, since the vault is local files first

OpenEye, Cadence Molecular Sciences

  • The free Public Domain Research Licence requires surrendering intellectual property rights and publishing results into the public domain, which rules it out for any academic group with a technology transfer office or patent ambitions.
  • Free academic licences are renewable but re-evaluated annually with no guarantee of continuation, so a multi-year research programme has no assured software entitlement beyond the current year.
  • OpenEye now sits inside Cadence Design Systems, whose core business is chip design, so the roadmap and licensing culture are set by a company for which molecular sciences is one growth line among several.
  • Commercial pricing is entirely unpublished and structured as annual subscriptions with separate Orion compute, making total cost of a screening programme hard to forecast before contracting.
  • The toolkits assume real computational chemistry expertise; they are libraries and applications for specialists, not an interface a medicinal chemist can drive without training.

Pricing, plan by plan

Obsidian

Free
  • Obsidian Sync$4/month
    • Sync notes across devices
  • Obsidian Publish$8/month
    • Turn notes into a website

OpenEye, Cadence Molecular Sciences

On request
  • Commercial licence$undefined/year
    • Annual subscription priced through Cadence sales
    • Toolkits and applications licensed separately from the Orion platform
    • Orion compute billed on top of software entitlements
  • Academic Package$undefined/year
    • Paid annual subscription for university groups under ten members
    • Includes support
    • Researchers retain intellectual property rights
  • Public Domain Research LicenceFree
    • No cost
    • No support of any kind
    • No intellectual property rights retained

Which should you pick?

Choose Obsidian if

  • You need bidirectional linking.
  • You want to start without paying.
  • You work on Web, Windows, macOS, Linux, iOS, Android.
  • You also want graph view visualization.
Obsidian review

Choose OpenEye, Cadence Molecular Sciences if

  • You need omega.
  • You work on Linux, Windows, macOS, Web, API.
  • You also want rocs.
OpenEye, Cadence Molecular Sciences review

Questions people ask

Is Obsidian or OpenEye, Cadence Molecular Sciences better?
Neither clearly leads. Obsidian starts at Free and OpenEye, Cadence Molecular Sciences at On request, and user ratings are close enough to be indistinguishable. Choose on capability and platform support.
Which is cheaper, Obsidian or OpenEye, Cadence Molecular Sciences?
Obsidian has a free tier; the other does not. Paid plans start at Free for Obsidian and On request for OpenEye, Cadence Molecular Sciences.
Does Obsidian or OpenEye, Cadence Molecular Sciences run on more platforms?
Obsidian runs on Web, Windows, macOS, Linux, iOS, Android. OpenEye, Cadence Molecular Sciences runs on Linux, Windows, macOS, Web, API.
Can I use Obsidian for free?
Yes. Obsidian has a free tier, so you can try it without paying. OpenEye, Cadence Molecular Sciences starts at On request.
What is Obsidian best used for?
Obsidian is most often used for local-first markdown note taking with no account required, linking notes into a personal knowledge graph, syncing a vault across devices with end-to-end encryption on the paid add-on, publishing a public site from a vault. Of those, local-first markdown note taking with no account required and linking notes into a personal knowledge graph are not what OpenEye, Cadence Molecular Sciences is typically brought in for.
What can Obsidian do that OpenEye, Cadence Molecular Sciences cannot?
Obsidian covers Bidirectional linking, Graph view visualization, Markdown support, Local file storage. OpenEye, Cadence Molecular Sciences covers OMEGA, ROCS, ROCS X, Orion platform.

Answered from the vendors’ own pages

Obsidian: Is Obsidian free?

Yes. The core Obsidian application is 100% free for personal and commercial use with no limitations. You can use unlimited vaults and every core feature without payment.

Source
OpenEye, Cadence Molecular Sciences: Is OpenEye still OpenEye?

It trades as OpenEye, Cadence Molecular Sciences, and is part of Cadence Design Systems following acquisition. The product names OMEGA, ROCS and Orion continue.

Obsidian: What file format does Obsidian use?

Obsidian stores every note as a plain Markdown file. Because it uses standard Markdown instead of a proprietary format, your notes remain portable and can be edited with many other Markdown editors.

Source
OpenEye, Cadence Molecular Sciences: Can academics use it for free?

Yes, through the Public Domain Research Licence or a Teaching Licence, but both come with no support and no intellectual property rights. Keeping IP rights and support requires the paid Academic Package.

Obsidian: Can I collaborate with others in Obsidian?

The core application does not include built-in team collaboration features. However, Obsidian offers optional add-ons and can be used with version control systems or cloud storage for collaboration.

Source
OpenEye, Cadence Molecular Sciences: What is ROCS X?

A machine learning enabled extension of ROCS shape search, built on the Orion platform, aimed at screening chemical spaces in the trillions of molecules.

OpenEye, Cadence Molecular Sciences: Is commercial pricing published?

No. Commercial licences are annual subscriptions quoted through Cadence sales, with Orion compute charged separately.

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