Applications of AutoDock Vina Software

AutoDock Vina is an open-source program for molecular docking. It was originally designed and implemented by by Dr. Oleg Trott in the Molecular Graphics Lab (now CCSB) at The Scripps Research Institute. Vina is a command line program that can be used with Autodock Tools through a GUI interface, or executed from a Windows command prompt or a Linux terminal. Autodock Vina improves the average accuracy of binding pattern predictions, speeds up searches by using a simpler scoring function, and still provides repeatable docking results when dealing with systems of about 20 rotatable keys. Its usage is similar to Autodock 4, but omits the step of calling the AutoGrid program (required by the original Autodock 4). In general, AutoDock is more complicated to operate and has extremely strict requirements on the operating environment, while AutoDock Vina is relatively simple to operate. Compared to AutoDock, the average accuracy of its combined mode predictions is also higher.

Our Services Based on AutoDock Vina Software

Autodock Vina is one of the most widely used bioinformatics software for computational docking. On the Autodock Vina software platform, the scientists of CD ComputaBio can dock multiple ligands at the same time and dock a large number of ligands in batches.

• Different Types of Docking
  Our scientists can use Autodock Vina software to provide different types of docking services, including site-specific, blind docking, protein-ligands, and more.
• Editing Protein and Ligands
  Our scientists use Autodock Vina software to edit proteins and ligands, including their structural modifications.
• Molecular Screening
  We use Autodock Vina to screen large or small molecular libraries. Our molecular library capacity is up to 75,0000.
• Visualize Interactions Between the Receptor and the Ligand
  Our scientists can easily convert PDBs to PDBQT format, then use the Autodesk Tools GUI to visualize receptor and ligand interactions and analyze the results.
• Virtual Screening Results Analysis
  Our scientists can easily analyze virtual screening results based on the rigid and flexible docking properties of Autodock Vina.

Our Capabilities

AutoDock Vina achieves about two orders of magnitude speedup, while also significantly improving the accuracy of binding mode predictions. We can predict the binding mode of small molecules to proteins. Because it is used to screen virtual libraries of drug-like molecules for leads for further drug development.

Features of AutoDock Vina Software

• Accuracy
  Compared to AutoDock 4, AutoDock Vina significantly improves the average accuracy of binding mode predictions.
• Ease of Use
  Vina is designed in such a way that it does not require users to understand its implementation details, adjust obscure search parameters, cluster results, or understand advanced algebra (quaternions).
• Flexible Side Chains
  As in AutoDock 4, some acceptor side chains can be selected to be considered flexible during docking.
• Multiple CPUs/Cores
  Additionally, Vina can take advantage of multiple CPUs or CPU cores on the system to significantly reduce its runtime.
• Implementation Quality
  Vina avoids imposing artificial constraints such as the number of atoms in the input, the number of twists, the size of the search space, the exhaustiveness of the search, etc.