TagDock:an efficient rigid body molecular docking algorithm for three dimensional models of oligomeric biomolecular complexes with limited experimental restraint data

What is TagDock?
TagDock is an efficient rigid body molecular docking algorithm that generates three-dimensional models of oligomeric biomolecular complexes in instances where there is limited experimental restraint data to guide the docking calculations. Through “distance difference analysis” TagDock additionally recommends followup experiments to further discriminate  divergent (score-degenerate) clusters of TagDock’s initial solution models.

How is the TagDock Software different from other docking tools?
Existing software tools can be challenging to use and computationally expensive.  As a tool for experimentalists, TagDock is less encumbered with complex user parameters.  In an hour on a typical desktop workstation, TagDock can generate a million initial structural candidates, and perform detailed refinement on a few hundred of those that are most consistent with the experimental restraint data.

Who developed the TagDock software?
Jarrod A. Smith, Christopher W. Moth, Sarah J. Edwards, and Terry P. Lybrand, Department of Biochemistry, Department of Chemistry, Department of Pharmacology, and Center for Structural Biology,Vanderbilt University

How does it work?
Details are available in the peer-reviewed publication listed below:
TagDock: An Efficient Rigid Body Docking Algorithm for Oligomeric Protein Complex Model Construction and Experiment Planning., Biochemistry, 2013, 52 (33), pp 5577–5584;(PubMed Link)

What software needs to be installed for proper working of TagDock?
The NAB module in AmberTools (free software from ambermd.org), which in turn minimally requires the GNU development environment on Linux, or Amber-supported compilers for other platforms.

What computer platforms/operating systems are recommended for TagDock to work?
A RedHat or derivative variant of Linux is the recommended platform.  However, any platform supported by AmberTools should compile and execute TagDock.

What are the TagDock materials provided through this license?
The TagDock source code, user manual, examples, and associated materials necessary to run docking and distance difference calculations are provided in a gzipped tar archive.

What is the cost of TagDock license?
TagDock is provided free of charge to academic and not-for-profit institutions via our academic online licensing process for non-commercial research purposes. Once you have completed checkout with this item, you will receive an e-mail with download instructions. TagDock must be licensed commercially by users at for-profit institutions. Please provide the initial licensee information requested in this form, and a representative will contact you to review licensing options for your organization.

Inventors: 
Terry LybrandJarrod SmithChristopher MothSarah Edwards
Licensing manager: 
Masood Machingal

Featured Video

Vanderbilt Patent Activity

View Vanderbilt University Patents

CTTC on Twitter