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Submit AI-powered prediction jobs through OpenBio to analyze protein structures, design new molecules, and run complex computational biology analyses. Monitor your jobs in real-time and view interactive results directly in your workspace.
What are Predictions?Predictions are computational jobs that use state-of-the-art AI or traditional computational models and tools to analyze biological data. OpenBio handles all the technical infrastructure—you just describe what you want to analyze.

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Available Prediction Tools

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Structure Prediction

Boltz-2

Purpose: Protein-ligand co-foldingInput: Protein sequence + optional ligand structureOutput: Protein-ligand complex structure

Chai-1

Purpose: Multi-modal foundation model for molecular structure predictionInput: Proteins, DNA, RNA, ligands, glycansOutput: Molecular structure

SimpleFold

Purpose: Fast structure predictionInput: Protein sequence onlyOutput: Protein structure

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Protein Design

ProteinMPNN

Purpose: Design sequences for structuresInput: Protein backbone structure (PDB)Output: Optimized amino acid sequences

LigandMPNN

Purpose: Design protein bindersInput: Target protein + binding siteOutput: Potential binder sequences

ThermoMPNN

Purpose: Improve protein stabilityInput: Protein structureOutput: Thermostable variants

Pinal

Purpose: Design from text descriptionInput: Natural language descriptionOutput: Designed protein structure

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Docking & Analysis

GeoDock

Purpose: Protein-protein dockingInput: Proteins (PDB)Output: Protein-protein complex structure
You can always ask OpenBio to tell you more about a prediction tool.

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Submitting Prediction Jobs

The most natural way to submit predictions is through conversation: 
Predict the structure of this protein using Boltz-2:
MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL

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What Happens Next

1

AI Understands Your Request

OpenBio analyzes your message and selects the appropriate prediction tool
2

Parameter Confirmation

The AI may ask for clarification or confirm parameters before submitting
3

Job Submission

Your prediction is queued and assigned a unique job ID
4

Real-time Updates

Monitor progress through status updates in your chat
5

Results Delivery

When complete, results automatically appear in your research panel

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Through the Predictions Page

The support for submitting predictions through the predictions page is coming soon.

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Monitoring Your Predictions

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Job Status Tracking

Location: Research panel → Predictions tab, or click “Predictions” in top navigation
The jobs will show up in the predictions page. They can have the following statuses: 1. Queued: Waiting in line to start 2. Running: Actively processing on GPU servers 3. Completed: Successfully finished 4. Failed: Error occurred during processing

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Viewing Job Details

Click on any prediction job to see comprehensive information:
  • Job ID: Unique identifier for reference
  • Tool and Version: Which AI model was used
  • Submission Time: When job was submitted
  • Runtime: How long the job has been running
  • Input Parameters: What data was provided
  • Error Logs: For failed jobs (if applicable)
You can refresh the page to see the latest status of your jobs.

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Working with Results

The results are usually files that are automatically saved to your project’s filesystem. You can see them from the files tab or ask OpenBio to tell you more about them.
You can download the results from the files tab.

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Retrying Failed Jobs

If a prediction fails:
  1. Review Error Message: Check what went wrong
  2. Fix Input: Address the issue (format, missing data, etc.)
  3. Resubmit: Click “Retry” or create a new job
  4. Monitor: Watch the new job progress
OpenBio can help you troubleshoot the issue and retry the job for you.

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Best Practices

Before submitting:
  • Check sequence format (no invalid characters)
  • Verify file types are supported
  • Confirm required files are uploaded
OpenBio automatically validates the input and always asks you to confirm the parameters before submitting the job.
  • Fast prediction needed → SimpleFold
  • Highest accuracy → Boltz-2 or Chai-1
  • Multiple molecule types → Chai-1
  • Protein design → ProteinMPNN family
  • Protein-protein docking → GeoDock
Structure predictions take time. Don’t submit duplicates.
Keep an eye on running jobs. You can see the progress in the predictions page.
Always download critical results:
  • Local backup of important structures
  • Save analysis reports for documentation
  • Keep sequences and scores for reference

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Troubleshooting

Common causes:
  • Invalid sequence format
  • File size too large
  • Missing required parameters
  • Unsupported file type
Solution: Check error message, fix input, retry
Check:
  • Confidence scores (low = unreliable) where applicable
  • Input sequence was correct
  • Try different prediction tool
  • Compare with known structures if available
Solutions:
  • Look on Predictions page for completed jobs
  • Refresh the page if needed
  • Check the files tab for the results
  • Ask OpenBio to tell you more about the results

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Next Steps

Visualizations

Analyze and interact with prediction results

Workflows

Create automated prediction workflows

File Management

Organize prediction inputs and outputs

Tutorials

Step-by-step prediction tutorials