AutoDock Vina is a molecular docking program that predicts how a small molecule may bind to a protein by searching possible poses and ranking them with an empirical scoring function.
ProteinIQ supports Vina, Vinardo, and map-based AutoDock4 scoring, plus flexible residues, AutoDock4Zn preparation, hydrated docking, simultaneous co-docking, and independent batch runs. For larger virtual screens, consider AutoDock GPU.
On ProteinIQ, AutoDock Vina is most commonly used to:
Predict ligand binding modes in a known binding pocket
Rank a focused compound set against one receptor (virtual screening)
Compare binding hypotheses after small structural changes to prioritize compounds
Test whether a proposed binding site can accommodate a ligand with plausible geometry
How to use AutoDock Vina online
Upload the receptor and ligand, define the search box, review the scoring and search settings, and submit the run. Runtime depends strongly on box volume, ligand flexibility, exhaustiveness, flexible residues, and ligand count.
Inputs
AutoDock Vina requires two inputs: a protein receptor and a ligand (or multiple ligands with simultaneous co-docking and batch docking).
Input
Description
Protein (Receptor)
Upload .pdb, .ent, or an already prepared rigid .pdbqt, or fetch a 4-character PDB ID such as 1HSG. PDB/ENT inputs are prepared with Meeko. A prepared PDBQT is used directly and cannot also be split into flexible residues.
Ligand
Provide ligand input as SMILES text, a supported structure file (.pdbqt, .sdf, .mol, .mol2, .smiles, .smi, .txt, .csv), or fetch by PubChem. One ligand is used in Single ligand mode, Simultaneous co-docking accepts up to 5 ligands in one shared search, and Batch docking docks up to 10 ligands independently against the same receptor.
Vina docking mode
Single ligand runs one docking job, Simultaneous co-docking places multiple ligands in the same search space during one run, and Batch docking runs independent ligand jobs for focused virtual screening.
Job name
Optional label stored with the run to make repeated docking experiments easier to identify.
Ligand validation blocks metal-containing ligands and disconnected multi-fragment submissions in the standard Vina workflow. Those cases are better suited to GNINA or to a more specialized docking setup.
Settings
The default scoring and search values match Vina 1.2.7. Search-box coordinates still need scientific judgment: use a focused manual box when the binding site is known.
Setting
Description
Scoring function
Vina is the default general-purpose choice. Vinardo uses a modified empirical model often favored for virtual screening benchmarks. AutoDock4 uses the classical AutoDock4 force-field-style scoring and is the required option for hydrated ligand and zinc-specific workflows in this interface.
Docking mode
Dock performs a full search. Score only evaluates the submitted pose without searching. Local only refines the input pose locally. Randomize only generates randomized ligand placement without full docking output ranking.
Exhaustiveness
Search thoroughness from 1 to 64, with a default of 8. Larger values increase runtime but improve the chance of recovering lower-energy poses.
Number of poses
Maximum number of docked poses returned, from 1 to 50.
Energy range (kcal/mol)
Retains poses within the specified energy window from the best-ranked pose. Larger values preserve more alternative solutions.
Min RMSD between poses (Å)
Minimum structural separation between reported poses. Increasing this value reduces near-duplicate outputs.
Max evaluations
Caps scoring function evaluations. 0 leaves the choice to Vina's automatic internal heuristic.
Random seed
Integer seed for reproducible searches. 0 allows nondeterministic initialization.
Search mode
Manual passes explicit center and size values to Vina. Whole protein bounds is a ProteinIQ convenience that covers the receptor-coordinate bounds plus padding; it is not Vina's ligand-based CLI autobox and can create a very large search space.
Center X, Y, Z
Coordinates of the search-box center in Manual mode.
Size X, Y, Z
Search-box dimensions in Å. Smaller boxes are faster and usually more reliable when the binding site is already known.
Auto-box padding (Å)
Extra padding around receptor bounds in Whole protein bounds mode.
Grid spacing (Å)
Spacing used for affinity map discretization. Smaller spacing increases resolution at higher computational cost.
Force even voxels
Requests an even number of voxels for maps computed with Vina or Vinardo. AutoGrid GPF dimensions are always even.
Results
Upon successful docking, AutoDock Vina outputs several files. To make your research easier, ProteinIQ return displays the results in three different formats.
Output
Description
Structure
Interactive 3D view of the receptor and docked pose geometry
Data
Dock mode: affinity, RMSD bounds, and all five native energy terms. Score/local modes: Vina's named eight-term energy vector.
Files
Individual poses, native combined PDBQT, prepared receptor and ligand PDBQT, run summary, and hydrated dry/scored poses when applicable.
AutoDock Vina results on ProteinIQ showing the interactive 3D viewer of the receptor with a docked ligand pose next to the table of scored poses with binding affinity values in kcal/mol and downloadable pose files
The affinity score is most useful as a relative ranking within one consistent experiment. Absolute kcal/mol values should not be treated as direct binding free energies, especially across different targets, protonation states, or receptor preparations.
Pose geometry matters as much as score. A slightly worse score with sensible hydrogen bonding, steric fit, and ligand burial is often more credible than the top-ranked pose if that pose shows clashes or unrealistic exposure. For batch docking, comparisons are most meaningful when all ligands were prepared with the same protonation and tautomer assumptions.
How does AutoDock Vina work?
AutoDock Vina combines an empirical scoring function with stochastic global search and gradient-based local optimization. The ligand is translated, rotated, and flexed inside a predefined search volume; each candidate pose is scored; and promising conformations are refined before final clustering and ranking.
Scoring
The scoring function estimates binding favorability using weighted steric, hydrophobic, hydrogen-bonding, and penalty terms. Vina uses the default empirical model. Vinardo modifies the parameterization for improved enrichment in some screening benchmarks. AutoDock4 uses older force-field-style terms and is required when metal-aware behavior or hydrated ligand workflows are needed.
Search
Vina uses multiple independent runs initialized with random poses. Within each run it alternates broad perturbation steps with local refinement, then collects the best solutions across all searches. The Exhaustiveness parameter controls total independent search effort, while Number of poses and Energy range determine how many alternatives survive to the final report.
Flexible residue docking
Most docking calculations keep the receptor rigid apart from ligand torsions. When Flexible residues are specified, selected receptor side chains are allowed to move during the search. This can recover poses that rigid docking would miss, but increases the search space and runtime substantially. Flexible docking is usually reserved for a few residues with a clear mechanistic rationale for moving.
Limitations of the AutoDock Vina algorithm
Rigid receptor approximation: Whole-protein backbone motion is not modeled, so induced-fit effects can still be missed even when flexible residues are enabled.
Approximate scoring: Docking scores support prioritization, not definitive affinity prediction.
Preparation sensitivity: Protonation state, tautomer choice, bound waters, and search-box placement can change rankings substantially.
Metal handling: Standard Vina scoring is not a good default for zinc-dependent binding chemistry; use the AutoDock4Zn mode when its tetrahedral zinc model matches the system.
Large or highly flexible ligands: Search quality drops as conformational complexity increases, even when runtime is increased.
Hosted ligand limits: Each ligand is limited to 32 rotatable bonds, 150 heavy atoms, and 300 total atoms.
Fragment handling: Standard Vina blocks metal-containing ligands and disconnected multi-fragment submissions—use GNINA for those cases.
Unbound ligand energy
Optional unbound-system energy supplied to Vina Score only; leave its switch off to use Vina's calculated term.
Local optimization max steps
Maximum minimization steps for Local only; 0 uses Vina's movable-atom heuristic.
Flexible residues
Comma-separated residues such as A:315,B:42 to model selected side-chain flexibility during docking.
Hydrated ligand workflow
Uses Meeko water pseudo-atoms, Vina's mapwater.py, and dry.py for each returned pose. It requires AutoDock4 scoring, full Dock mode, and one ligand.
Zinc metalloprotein mode
Runs Vina's AutoDock4Zn pseudo-atom preparation and zinc parameter set. It requires AutoDock4 scoring.
Disable post-docking refinement
Skips explicit-receptor refinement for Vina or Vinardo. Vina does not apply this option to AutoDock4 scoring.
Use custom scoring weights (advanced)
Unlocks every weight accepted by Vina's selected scoring function, including macrocycle glue and rotational terms.
