Overview

What Docking Studio does

Docking Studio runs AutoDock Vina 1.2.7, compiled to WebAssembly, inside your browser. Load a receptor from the PDB, AlphaFold DB or a file, give ligands as SMILES, SDF, MOL2 or a PubChem name, and the studio prepares both (protonation at pH 7.4, Gasteiger charges, PDBQT, 3-D conformers), sets the box from a co-crystal ligand, residues or coordinates, and docks.

Poses open in a 3-D viewer with an interaction profile (hydrogen bonds, hydrophobic contacts, salt bridges). A redocking benchmark on 42 complexes puts 35.7 % of top poses within 2 Å of the crystal pose, with scores identical to native Vina on the same inputs.

Technical specifications

Inputs: PDB ID / AlphaFold DB / PDB or mmCIF file · SMILES, SDF, MOL2 or PubChem name
Outputs: Docked poses (PDBQT, SDF) · Affinity table (CSV) · Interaction profile
Engine: AutoDock Vina 1.2.7 (WebAssembly, threads when cross-origin isolated) + RDKit + TypeScript preparation
Platforms: Chrome, Edge, Firefox and Safari (current versions) · Windows, macOS, Linux and ChromeOS · No installation, no account, no upload
Limits: Rigid receptor, one box up to 40 Å, ligands up to 70 heavy atoms and 20 rotatable bonds, up to 300 compounds per screen; scores are estimates, not binding free energies
Licence: Free during the public preview; institutional licences on request

Features

Capabilities

01

Real AutoDock Vina

Vina 1.2.7 in WebAssembly, multi-threaded when the browser allows it; scores match native Vina.

02

Receptor and ligand preparation

pH 7.4 protonation, Gasteiger charges and PDBQT, from PDB, AlphaFold DB, SMILES, SDF, MOL2 or PubChem.

03

Box set-up

From a co-crystal ligand, a list of residues or explicit coordinates.

04

Poses and interactions

3-D pose viewer, affinity table, RMSD to a crystal pose and an interaction profile.

05

Small virtual screens

Dock up to 300 compounds and rank them, with results exported as CSV and SDF.

06

Validated

Redocking benchmark on 42 complexes, published with the source code.

Use cases

Who uses it, and for what

Docking a ligand into a target before ordering compounds
Teaching molecular docking in a classroom without installing software
Ranking a small set of analogues against a binding site

Documentation

Quick start

Open Docking Studio
Use the button on this page or the Workbench menu. Nothing to install; works in current Chrome, Edge, Firefox and Safari.
Load data or the demo
Drop in your files (PDB ID / AlphaFold DB / PDB or mmCIF file, SMILES, SDF, MOL2 or PubChem name) or load the labelled synthetic demo to explore safely.
Run and inspect
Results appear as interactive figures and tables; each analysis records its parameters and versions.
Export and cite
Export figures and tables, add them to a report, and copy the auto-written methods paragraph.

Full documentation

Learn the methods with Vedicgen