Applications of AutoDock Software


Applications of AutoDock Software

AutoDock is a molecular modeling simulation software. It is particularly effective for protein-ligand docking. AutoDock is one of the most cited docking software applications in the research community. AutoDock software consists of two programs, AutoGrid and AutoDock. Among them, AutoGrid is mainly responsible for the calculation of relevant energy in the grid, while AutoDock is responsible for conformation search and evaluation. AutoDock runs on Linux, Mac OS X, SGI IRIX and Microsoft Windows. It is available as a package on several Linux distributions, including Debian, Fedora, and Arch Linux. AutoDock includes but is not limited to, the following applications: X-ray crystallography, structure-based drug design, lead compound optimization, virtual screening, combinatorial library design, protein-protein docking, and chemical mechanism studies.

Our Services Based on AutoDock Software

On the AutoDock software platform, CD ComputaBio adopts an interdisciplinary approach, bringing together researchers in structural biology, computational modeling, visualization, and biomedical applications to provide convenient information services to researchers in various industries.



CD ComputaBio develops new methods for predicting small molecule-biomolecule interactions for drug design, discovery, and virtual screening. We support flexible docking, rigid docking, semi-flexible docking.



Developing extensible, interoperable methods is to explore multiscale representations of biomolecular systems, with virtual, tactile and augmented reality modalities.



We support the design and virtual screening of protein covalent inhibitors, the docking and binding energy prediction of small molecules and peptides to flexible biomolecular targets, and the modeling of cellular structures.

Our Capabilities

  • Binding Site Prediction
  • Computational docking is widely used to study protein-ligand interactions as well as drug discovery and development.The scientists of CD ComputaBio uses AutoSite and AutoLigand to predict binding sites. They are is programs that predicts the optimal site for ligand binding to receptors.

  • 3D Integrative Models of Cellular Environments Creation
  • We are currently exploring new methods based on AutoDock to create 3D comprehensive models of cellular environments and whole cells to bridge the experimental gap between molecular structure and cellular function.

  • Result Evaluation
  • We evaluate the results according to different docking needs. Parameterization of AutoDock scoring function is available to the user to adjust for a specific system if required. AutoDock Vina scoring function is highly approximate, with spherically symmetric hydrogen bonding potentials, implied hydrogens, and no electrostatic contributions.

Features of AutoDock Software

AutoDock is a suite of free, open-source software for computational docking and virtual screening of small and macromolecular receptors. The kit currently includes several complementary tools:

  • Autodock
  • Autodock is effective for general docking and virtual screening of ligands to biomolecular targets, and specialized functions can be used to predict covalent ligand complexes, ligands with flexible loops, explicit hydration, and metalloprotein targets.

  • AutoDock Vina
  • AutoDock Vina is a turnkey computational docking program based on a simple scoring function and fast gradient-optimized conformational search. It can rapidly and efficiently dock drug-like ligands with protein targets.

  • AutoDockFR
  • AutoDockFR is a computational docking program with flexible protein targeting, including side chain movement and induced fitting.

  • AutoDockCrankPep
  • AutoDockCrankPep is a program for computational docking of peptides to protein targets.

Related Links

Autodock Tutorial

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