MOLARIUM · molecular studioAll reproductionsSource repository

SOS1: designer intent and receptor response

Follow the hit-to-BAY-293 series in the real Molarium interface. Declare the ligand's direction and contact, hold it fixed, and test whether Phe890 can move out of its path.

Molarium paper — ChemRxiv-submitted v1

Rafal Wiewiora and Woody Sherman · . The exact author-supplied PDF submitted to ChemRxiv, including the SOS1 example and technical appendices.

Read submitted v1 (PDF)

Final LaTeX and figures · Version and SHA-256 record · Manuscript history and review

1. Recompute the story

Run all 159 scientific actions in your browser, including 13 fixed-coordinate Phe890 energy calculations and the BAY-293 continuation. Requires WebGPU and several minutes.

Open recomputable replay

2. Inspect saved states

Review seven exact full-system checkpoints without recalculation. Play, pause, and use the arrows to compare the ligand placement and Phe890 response.

Open precomputed replay

3. Watch the movie

A 63-second tour of the saved checkpoints, with one-second popups for the recorded calculation steps. No calculations are rerun.

Watch MP4

Checkpoint movie

Loading the movie for smooth forward and backward seeking…

Download checkpoint MP4

This demonstration is reference-informed: the crystal series was inspected to infer designer intent. Later crystal coordinates were not imported as design targets. The predicted response is a Phe890 side-chain flip; Tyr884 supplies the backbone contact. Source waters are retained. Recalculation can change numerical coordinates and energies; the saved checkpoints preserve the exact paper results.