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Release Notes🔗

Apheris Hub 0.3.1🔗

  • Release date: 2025-09-12

Co-folding application: 0.11.1🔗

  • Boltz-2
    • boltz2:0.11.1
    • boltz2:0.11.1-public-colabfold
  • Mock Model
    • mock:0.11.1
    • mock:0.11.1-public-colabfold
  • OpenFold 3
    • openfold3:0.11.1-public-colabfold

Highlights🔗

The Apheris Hub 0.3.1 release introduces significant enhancements to the Apheris Hub with focus on protein structure analysis and user experience improvements.

New Features🔗

  • MSA Server Configuration: Users can now use different Multiple Sequence Alignment (MSA) servers for structure prediction.

MSA Server Options:

  • Pre-Generated MSA: The base models assume the user will upload pre-generated MSA files; this is the most local option, making no calls outside the Hub to any MSA server.
  • Apheris-hosted Foldify: The base model now supports using a Foldify server, and for a limited time, comes pre-configured with an Apheris-hosted option for free, intended only for evaluation use. This server should be treated as a public MSA server, and users should take the same precautions when using it as they would, for example, the public ColabFold Server.
  • Self-hosted Foldify: You can also configure the Hub to use your own internally hosted Foldify server; adding ColabFold servers is coming soon. Please contact Apheris for support in setting up your own Foldify server via support@apheris.com.
  • Public ColabFold: Until support is available for configuring access to ColabFold servers, there is a public-colab-fold model option that generates MSAs via the public ColabFold server, which is not hosted by Apheris.
  • Real-time Model Installation Feedback: Added progress indicators for model installation, showing percentage completion and status updates in real-time. If installation issues occur, error messages are displayed with troubleshooting information available in model settings.
  • Structure Visualization with Mol: Migrated to Mol for rendering 3D molecules, delivering enhanced visualization and interaction capabilities.

Enhancements🔗

  • Improved 3D Molecule Visualization:

    • Adopted Mol* for rendering 3D molecules, providing better visualization capabilities and performance.
    • Enhanced molecule coloring and added Chemical Component Dictionary (CCD) code lookups for improved annotation.
    • Removed background from molecule viewer and added hover information for better visualization.
    • Added legend and units for matrix view to improve data interpretation.

  • User Interface Improvements:

    • Added unique naming for downloaded results to prevent filename conflicts and improve organization.
    • Redesigned the job form for a more intuitive user experience.
    • Added job ID display in result list for easier tracking.
    • Enhanced offline connection status indication for better user feedback when connectivity is lost.
    • Duration formatting improved to show minutes and seconds instead of just seconds.
    • Updated model naming conventions to clearly reflect MSA server options. Models now indicate whether they use the public ColabFold server, providing transparency about external dependencies.

  • Inference Runs / Results Improvements:

    • Enhanced sequence selection highlighting for precise amino acid selection.
    • Added catching of MMSeqs2 MSA server errors from Boltz-2 model.

Bug Fixes🔗

  • UI and Configuration

    • Improved error formatting for MSA linting.
    • Updated schema validation to properly handle MSA field requirements.

  • Inference Runs / Results Improvements:

    • Clarify error messages for mock model inference results when non default inputs are used.
    • Fixed OpenFold3 pLDDT vectors for improved accuracy.

Apheris Hub 0.2.1🔗

  • Release date: 2025-08-22

Co-folding application: 0.10.1🔗

  • Boltz-2
    • boltz2:0.10.1-private-msa
    • boltz2:0.10.1-public-msa
  • Mock Model
    • mock:0.10.1-private-msa
    • mock:0.10.1-public-msa
  • OpenFold 3
    • openfold3:0.10.1-public-msa

Highlights🔗

  • Enhancements
    • Detection of API connection loss on the UI
  • Bug Fixes
    • Labels are now shown on the PAE/PDE Plot
    • ColabFold server unavailability error messages are clearer when using Boltz-2

Apheris Hub 0.2.0🔗

  • Release date: 2025-08-08

Co-folding application: 0.9.0🔗

  • Boltz-2
    • boltz2:0.9.0-private-msa
    • boltz2:0.9.0-public-msa
  • Mock Model
    • mock:0.9.0-private-msa
    • mock:0.9.0-public-msa
  • OpenFold 3
    • openfold3:0.9.0-public-msa

Highlights🔗

The Apheris Hub provides local access to AI-based drug discovery applications. Applications deployed in the Apheris Hub are designed to run entirely locally or in your private cloud or on-prem environments - such that no data ever leaves your environment. They integrate into enterprise R&D stacks and extend rather than replace existing scientific workflows.

Applications in the Apheris Hub focus on a set of drug discovery tasks and are based on one or more foundation models.

Our first application is focused on Co-Folding, starting with inference - including input validation, and batch execution either programmatically via an API or manually with a scientist-friendly GUI.

The Apheris Co‑Folding Application is a secure, locally hosted tool for using co‑folding models on sensitive proprietary data. By running Boltz-2 and OpenFold3 on in‑house targets, researchers can assess model accuracy in their specific domain and easily integrate these models into their wider workflows. The product provides visualization tools, streamlined data preparation support, and generates auditable, reproducible records for use in regulated environments.

Upcoming Improvements🔗

Our first release is designed to support early evaluation and adoption of OpenFold3, and we are already making many improvements for follow-up releases. We are investing in more powerful visualizations, more models, job management, and supporting fine-tuning locally and via secure federation.

We plan to release additional support for data preparation, benchmarking, and fine-tuning in our early pipeline. We can already support integrating these models into your existing benchmarking pipelines, but we'd like to add more to ensure the biggest impact on your benchmarking efforts. We'd love to hear any feedback you have around this as well. Please feel free to reach out with feature requests, comments, or suggestions at support@apheris.com.

In future versions, we will allow pointing to an existing private MSA server for OpenFold3. However, today Apheris can also help you set up a private MSA server if you wish. In that case, please contact us at support@apheris.com.

For the first release, submitting additional jobs will put those jobs in a queue. The GPU is fully consumed per job; parallelism and multi-GPU support will come with follow-up releases. The current architecture was built for simplicity in deployment and configuration with more flexibility and scalability coming very soon.