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Smina: Molecular Docking, Custom Scoring and Energy Minimization Built on AutoDock Vina
smina is a fork of AutoDock Vina that focuses on improved scoring and energy minimization for molecular docking. The SourceForge project page describes it as customized for scoring function development and high-performance energy minimization, and lists David Koes at the University of Pittsburgh as maintainer. The page states that smina is not directly affiliated with the AutoDock project. The code is available on SourceForge and GitHub.
Docking programs predict how a small molecule sits in a protein binding site and score the result. The smina README presents the tool as a Vina variant for researchers who need more control over how poses are scored and minimized, for example when developing or testing scoring functions.
Property | Detail |
|---|---|
Type | Fork of AutoDock Vina (version 1.1.2 per the README) |
Focus | Scoring function development and energy minimization |
Ligand formats | Broad support through OpenBabel, including multi-ligand files such as SDF |
Receptor input | PDBQT |
Maintainer | David Koes, University of Pittsburgh (SourceForge page) |
License | GPLv2 on SourceForge; the GitHub README lists dual Apache-2.0 and GPL-2.0 |
What Smina Adds to AutoDock Vina
The README lists these changes relative to standard Vina:
Ligand format support: many ligand formats through OpenBabel, plus multi-ligand files.
Additional scoring terms: extra term types such as desolvation and electrostatics.
Custom scoring: user-parameterized scoring functions through a custom scoring option, and alternative built-in scoring such as Vinardo.
Automatic box creation: the search box can be built from a user-specified bound ligand.
More poses: output of more than 20 docking poses.
Minimization: improved minimization that runs to convergence.
Flexible residues: experimental support for flexible receptor side chains.
Smina Speed and Scoring Options
Aspect | README statement |
|---|---|
Local minimization workflows | Much easier to use and 10 to 20 times faster than Vina |
Docking performance | Roughly the same as Vina |
Score-only and local search | Available as options |
Per-atom interaction terms | Available as output |
Configurable Search and Output
The README groups options for the search space (center and size, or an automatic box around a ligand), scoring and minimization, output (file format set by extension, log file), and miscellaneous controls such as CPU count, random seed, exhaustiveness, number of binding modes, energy range and automatic hydrogen addition.
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Accelerating Discovery with Smina on Tamarind Bio
Docking and rescoring: dock small molecules to a protein or score existing poses with score-only mode.
Pose minimization: refine ligand poses by energy minimization to convergence.
Scoring function experiments: compare built-in scoring such as Vinardo or a custom function.
Multi-ligand runs: process files that contain many ligands.
How to Use Smina on Tamarind Bio
Log in: sign in at tamarind.bio and open the Smina tool.
Provide the receptor: supply the protein structure; smina reads PDBQT receptors, and the platform may handle conversion.
Provide ligands: upload one or more ligands, for instance as an SDF file, if exposed.
Define the search region: set a center and size, or use a bound reference ligand to build the box automatically, if exposed.
Choose the scoring mode: select the default, an alternative such as Vinardo, or score-only or minimize modes, if exposed.
Run the job: submit it and wait for completion.
Download outputs: retrieve the poses and scores.
Interpret and follow up: inspect top-ranked poses and use the results to prioritize compounds.
Things to Keep in Mind
The README describes flexible receptor residues as experimental.
The README says docking performance is roughly the same as Vina; the speed gain applies to minimization workflows.
The SourceForge page lists the project status as Beta.
The README directs users to the original SourceForge project for support and issues.
Source: smina project README (github.com/mwojcikowski/smina) and project page (sourceforge.net/projects/smina). The README asks users to cite the smina paper at pubs.acs.org/doi/abs/10.1021/ci300604z.