Docking & Binding · Scripps Research
AutoDock Vina
Predicts small-molecule binding poses and affinity scores against protein structures.
What AutoDock Vina is
AutoDock Vina is a molecular docking and virtual screening tool developed by Scripps Research. It evaluates how small-molecule ligands interact with protein receptors, determining where a compound is likely to bind and scoring the quality of that fit.
It acts as a widely recognised benchmark within structural computational chemistry, producing predicted binding affinities quantified as docking scores in kilocalories per mole.
How it works
AutoDock Vina explores candidate ligand conformations within a specified search volume on a receptor structure. If an existing ligand is present in the receptor structure, the search box can be centred directly upon it; alternatively, explicit coordinates can be supplied, or the search can encompass the entire protein surface.
The engine assesses candidate poses using an established scoring function to quantify binding affinity and returns the top-scoring conformations.
Key facts
- Version
- 1.2.7
- Domain
- Docking
- Supported tasks
- Molecular docking, virtual screening
- Input modalities
- Protein structure, small molecule
- Hardware requirement
- Runs on CPU
What you can use it for
- Molecular docking
- Search for preferred binding poses of a candidate small molecule within a targeted protein binding site and determine the corresponding score.
- Virtual screening
- Evaluate small molecules against a receptor target to rank their fit and estimated binding energies.
- Whole-protein exploration
- Explore the entire surface of an unbound receptor to identify potential binding sites when specific pocket coordinates are unknown.
Run it here
No installation and no GPU of your own: fill in the inputs and it runs on our servers. Results stay in your browser unless you sign in.
Runs on On-demand CPU
Runs on our servers with on-demand compute. A first run needs time to load the model; active capacity can be reused and scales down when idle.Run this model
AutoDock Vina
Strengths and limits
Good at
- Serves as an established baseline scoring function widely recognised across molecular docking research.
- Outputs complete all-atom coordinates in standard PDB format along with quantitative scores in kcal/mol.
- Executes on CPU hardware without requiring specialised accelerator cards.
Watch out for
- Searching the entire protein rather than a targeted binding box produces weaker claims regarding true binding site location.
- Requires manual definition of search box centre and size when no co-crystallised ligand is present in the input receptor.
Inputs and outputs
You provide
Receptor (PDB or entry code)
Coordinates, or a code such as 1IEP.
Ligand SMILES
Canonical SMILES for the small molecule.
Search box centreoptional
Three numbers, e.g. 14.1 75.1 37.4. Defaults to any bound ligand in the structure.
Search box size (A)optional
Exhaustivenessoptional
Higher searches harder and costs proportionally more.
Poses to returnoptional
You get back
All-atom coordinates in PDB format, viewable and downloadable.
Poses with Vina score in kcal/mol.
Licence
Commercial use permitted · Apache-2.0
The Apache-2.0 licence allows use in commercial research and products.
Questions
Can I use AutoDock Vina commercially?
Commercial use permitted. The Apache-2.0 licence allows use in commercial research and products.
How do I run AutoDock Vina without installing anything?
Use the form under “Run it here” on this page: fill in the inputs and press Run model. It runs on our servers, typically in 15s, and a run costs about 14 credits. Visitors without an account get 1,000 credits a month.
What inputs does AutoDock Vina require?
It requires a receptor provided as a PDB structure or entry code and a ligand provided as a SMILES string, alongside search parameters including the box centre, box size in angstroms, exhaustiveness level, and the number of poses to return.
What outputs are produced?
It returns downloadable all-atom coordinates in PDB format and a table of poses annotated with their Vina score in kcal/mol.
How is the search space defined?
If the receptor structure already contains a bound ligand, the search box is positioned around that ligand. Alternatively, specific spatial coordinates can be specified or the search can cover the whole protein.
Does AutoDock Vina require specialised hardware?
No, it runs on standard CPU hardware.
Written from AutoDock Vina's own documentation. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.