Molecular docking is a core tool in drug discovery, and now that virtual screening capability has scaled up dramatically, it's producing far more candidate structures than teams can realistically review by hand — putting real pressure on downstream structure-activity analysis to keep up.
In practice, tools like Benchora (an AI drug-design agent) already surface binding interactions automatically once docking finishes, feeding that straight into the next round of structure modification. But a lot of research teams still prefer to re-check binding interactions themselves before committing to a modification — confirming the key contacts, then deciding what to change based on real experience. To support that workflow directly, ChemOrchestra recently added a dedicated structure-activity analysis feature. Here's the three-step version:
ChemOrchestra: www.quantabricks.xyz
Step 1: Dock, Co-fold, or Screen
Start from a pre-built tool on the homepage.
Draw your molecule, pick a ligand, and run docking (or co-folding) — the workflow is the same as a standard docking or co-folding run.
(These two options are docking and screening, respectively.)
Step 2: View the Interactions
3D interaction view, suited for reports and paper figures.
Structure-activity analysis is rendered as a 2D diagram — similar to LigPlot+ — projecting the protein-residue interactions onto a flat layout. SVG export is supported.
(KRAS–MRTX1133 interaction analysis)
Step 3: Edit the Interaction Diagram
Click Edit to enter edit mode — adjust residue positions, font size, and label direction.
Note: Pocket hydrophilic/hydrophobic coloring and ligand structure can't be edited, to keep computed results reproducible and strictly defined. Residue labels are fully customizable.
Don't forget to save the SVG if you're dropping it into a paper.
ChemOrchestra supports enterprise deployment for this feature. If that's relevant to you, related reading:
Benchora: an AI decision agent for BD-ready molecular design
Common docking mistakes and how to avoid them
Fast binding-pocket identification
Also worth checking out: LightCone's new LigandView feature, built for anyone doing covalent-inhibitor design — edit a ligand directly inside the binding pocket, then export it straight to mmCIF/PDB.
ChemOrchestra: www.quantabricks.xyz
LightCone: https://lightcone.quanta-bricks.com/
Feel free to schedule a meeting with me if you have any specific questions/requests: https://calendly.com/yizhouma/chemorchestra-user-session
Join our community to learn more: https://discord.gg/u3Mb6C2aHv