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Overview

Once you’ve run a high throughput virtual screen, the next step is to analyze the results at scale and downselect your compounds. This tutorial covers that full downselection workflow in RevStudio’s Compound Review — starting from your RevScreen (static, flexible, or ensemble docking) or Boltz2 results, and going all the way through to a 3D pose-level review that your medicinal chemistry team can use to sign off before compounds move to the wet lab. Unlike a purely 2D triage, this workflow pulls the actual top-ranked 3D poses for each compound directly from the pipeline they were generated in, so your team can review binding mode alongside 2D structure in a single collaborative session.
Downselecting Compounds After High Throughput Screening — Watch Video

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When to Use This Workflow

Use this workflow any time you’ve run one or more screening campaigns or batches and need to downselect to a smaller, high-confidence compound set — with 3D poses in hand — before moving to review or synthesis:
  • RevScreen — Static & Flexible Docking
  • RevScreen — Ensemble Docking
  • Boltz2 Cofolding
If you’ve run multiple campaigns or batches, you can select and download several at once, run your own analysis externally (or in RevAgent), and then bring your downselected list back into RevStudio for 3D-aware review.

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Step 1: Export and Downselect Your Results

1

Open your docking engine

From the Engines tab, open RevScreen (or Boltz2) and go to the analysis view for your campaign.
2

Select your batches or campaigns

If you’ve run multiple campaigns or batches, select the ones you want to pull results from. You can download and combine several batches at once.
3

Export your data

Export the compound activity metrics, confidence scores, and any other data you need from RevScreen or Boltz2 as a CSV.
4

Filter and downselect

Concatenate your exported CSVs if needed and run your own filtering — the goal is to land on a downselected list, typically somewhere in the range of 50–200 compounds, that’s ready for downstream review.
5

Confirm your SMILES column

The only field you strictly need in your final CSV is a column of SMILES strings. Login IDs, affinities, pose counts, and other metrics can all ride along in the same file.

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Step 2: Create a Compound Review Session with Poses

With your downselected CSV ready, head to RevStudio → Compound Review to bring the compounds — and their 3D poses — into a shared review session.
1

Decide: 2D only, or 2D + 3D

If you only need to review compounds at the 2D level, you can upload your CSV directly. If you want to pull the actual 3D poses generated for each compound, use Import from Pipeline instead.
2

Create a new review

Click Import from Pipeline and create a new review. Give it a clear name and, optionally, a description.
3

Set a downselection filter (optional)

You can filter based on top percentage of performers overall, top percentage within the pipeline, or a fixed top number of compounds — downselection thresholds are calculated on the docking results (e.g. static/flexible ensemble docking affinities).
4

Select the source campaign

Choose the campaign or pipeline your compounds came from.
5

Upload your SMILES CSV

Upload the SMILES CSV with your associated data, then click Search Pipeline. RevStudio will match your compounds against the full pipeline and report how many matched (for example, 487 of 800 compounds).
6

Create the review

Click Create Review. RevStudio pulls all matched compounds — along with their top-ranked poses — into a structured review session.

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Step 3: Review Compounds in 2D and 3D

Inside a review session, you can switch between a tabular view and a grid view. Grid view is the most common choice for stepping through compounds one at a time with full context visible.

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Working Through the Compound Set

1

Click through your compounds

Use the grid view to click through each compound and review its data, 2D structure, and associated metrics.
2

Share the session

Click Share to give teammates in your organization access. Shared sessions appear under their Shared with Me tab, and all changes either of you make are reflected in the same collective session.
3

Add comments

Comment directly on a compound to record your assessment. Comments are attributed to their author, and you can edit or delete your own comments as the review progresses.
4

Flag compounds

Flag compounds you and your collaborators want to downselect further, then filter the session to show only flagged compounds.
5

Filter by properties

Filter on pose count or any other computed metric to narrow down the set you’re actively evaluating. Filtered results update both the grid and the 2D structure side panel.

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Reviewing the 3D Pose

1

Open the 3D profile

Each compound imported via pipeline comes with an associated 3D profile — the pose pulled from the source campaign.
2

View the 3D pose

Click View 3D Pose to open a larger, more refined view of the binding pose, including core interactions — whether the pose came from Boltz2 or a static/flexible ensemble docking pipeline.
3

Pop out for a bigger view

Pop the 3D viewer out to expand it further and get a clearer look at the interactions.
Currently, only one pose is shown per compound. Support for viewing all of an engine’s top nine generated poses is planned.
4

Annotate as you go

While reviewing the 3D pose, you can still write notes, like/dislike the compound, and add tags — for example, flagging that a compound engages certain amino acids, or that it’s non-synthesizable.

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Step 4: Configure Tags

Tags help you categorize compounds against structural or mechanistic criteria as you review.
1

Open tag configuration

Use the tag panel to create, edit, or turn off tags.
2

Customize color schemes and icons

Assign colors and icons to tags so they’re easy to scan at a glance across the grid view.

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Step 5: Head-to-Head Compound Comparison

When you need to compare a handful of compounds side by side:
1

Select your compounds

Choose the compounds you want to compare — for example, three or six candidates you’re deciding between.
2

Open the Compare tab

Pull them all into the Compare tab to view them simultaneously and make your assessment across the set.
3

Return to the full review

Click Back to Review at any point to return to the full compound list and continue your session.

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Why This Matters

This workflow turns a large, multi-batch screening output into a tight, well-documented compound set ready for the wet lab:
  • Downselect from hundreds of thousands of screened compounds down to a manageable shortlist using your own filtering criteria
  • Bring 2D structure and top-ranked 3D poses into the same collaborative session, so reviewers aren’t switching tools to judge binding mode
  • Capture flags, tags, comments, and likes/dislikes as a structured, shared record of why a compound advanced or didn’t
  • Use head-to-head comparison to make final calls across your top candidates before triaging to the wet lab in RevLab

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Next Steps