TagDock is an innovative molecular docking tool developed at Vanderbilt University’s Center for Structural Biology. Designed for researchers studying biomolecular complexes, it offers efficient, user-friendly solutions for generating 3D models with limited experimental data. The FAQs below address TagDock’s functionality, requirements, and licensing. For further assistance, visit our Contact Us page or explore licensing options.
What is TagDock?
TagDock is an efficient rigid body molecular docking algorithm that generates three-dimensional models of oligomeric biomolecular complexes when experimental restraint data is limited. Using “distance difference analysis,” it recommends follow-up experiments to refine divergent solution models, enhancing research accuracy.
How is TagDock different from other docking tools?
Unlike other docking tools, TagDock is designed for experimentalists with simplified parameters, making it user-friendly. It’s computationally efficient, generating 1 million structural candidates and refining hundreds in about an hour on a standard desktop, streamlining complex biomolecular modeling.
Who developed TagDock?
TagDock was developed by Jarrod A. Smith, Christopher W. Moth, Sarah J. Edwards, and Terry P. Lybrand at Vanderbilt University’s Departments of Biochemistry, Chemistry, Pharmacology, and Center for Structural Biology.
How does TagDock work?
TagDock uses a rigid body docking algorithm to model biomolecular complexes, leveraging limited experimental data. For detailed methodology, see the peer-reviewed publication: TagDock: An Efficient Rigid Body Docking Algorithm for Oligomeric Protein Complex Model Construction and Experiment Planning, Biochemistry, 2013, 52(33), 5577–5584, available at PubMed.
What software is required to run TagDock?
TagDock requires the NAB module in AmberTools, a free software package available from ambermd.org. On Linux, it needs the GNU development environment; other platforms require Amber-supported compilers.
What computer platforms or operating systems are recommended for TagDock?
RedHat or derivative Linux distributions are recommended for optimal performance. However, any platform supported by AmberTools should successfully compile and run TagDock.
What materials are provided with a TagDock license?
The TagDock license includes source code, a user manual, example files, and associated materials in a gzipped tar archive, enabling docking and distance difference calculations for biomolecular research.
What is the cost of a TagDock license?
TagDock is free for academic and not-for-profit institutions via our academic licensing process for non-commercial research. After checkout, you’ll receive an email with download instructions. For-profit institutions must request a commercial license quote, and a representative will contact you to discuss options.