Docking & Binding · Koes Lab
SMINA
A molecular docking tool optimised for fragment-sized ligands and custom scoring functions.
What SMINA is
SMINA is a molecular docking program developed by the Koes Lab as a fork of AutoDock Vina. It is specifically designed to handle molecular docking and fragment docking tasks, providing enhanced capability for fragment-sized chemical ligands compared to standard AutoDock Vina.
The tool allows researchers to expose, adjust, or substitute terms within the scoring function. It outputs all-atom structural coordinates alongside ranked binding poses, making it suited for fragment-based drug discovery campaigns.
Key facts
- Version
- 2020.12
- Domain
- Docking
- Tasks
- Molecular docking, fragment docking
- Hardware
- CPU
What you can use it for
- Fragment-based ligand docking
- Dock small, fragment-sized molecules into receptor binding sites with performance tailored beyond standard Vina.
- Custom scoring molecular docking
- Evaluate protein-ligand binding poses using modified or user-selected scoring function terms.
- Receptor binding pose sampling
- Generate and rank multiple all-atom ligand binding conformations within a user-defined search box.
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
SMINA
Strengths and limits
Good at
- Handles fragment-sized ligands more effectively than stock AutoDock Vina.
- Exposes scoring function terms so they can be tuned or replaced.
- Runs on standard CPU hardware.
Watch out for
- Requires manual definition of the search box centre and dimensions.
- Restricted to CPU execution without GPU acceleration noted.
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.
Scoring functionoptional
Search box centreoptional
Three numbers. Defaults to any bound ligand in the structure.
Search box size (A)optional
Exhaustivenessoptional
Poses to returnoptional
You get back
All-atom coordinates in PDB format, viewable and downloadable.
Poses ranked by the chosen scoring function.
Licence
Commercial use permitted · Apache-2.0
The Apache-2.0 licence allows use in commercial research and products.
Questions
Can I use SMINA commercially?
Commercial use permitted. The Apache-2.0 licence allows use in commercial research and products.
How do I run SMINA 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 4.0s, and a run costs free. Visitors without an account get 1,000 credits a month.
What inputs are required to run SMINA?
It requires a receptor structure in PDB format or entry code, the ligand represented as a SMILES string, search box coordinates (centre and size in Ångströms), a selected scoring function, exhaustiveness settings, and the number of desired poses.
How does SMINA differ from stock AutoDock Vina?
SMINA is a fork of Vina that allows users to customise or alter scoring function terms and provides improved handling for fragment-sized compounds.
What outputs does SMINA produce?
It provides all-atom coordinates in PDB format along with a table of poses ranked according to the chosen scoring function.
Written from SMINA's own documentation. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.