Application of Visualization and Haptic Feedback to Enhance Molecular Docking

Principal Investigator: Dr. David R. Bevan, Department of Biochemistry

Co-Principal Investigators:
Dr. Layne T. Watson, Department of Computer Science
Dr. Ronald D. Kriz, Department of Engineering Science and Mechanics, and
Director of the University and Visualization Group ("VT-CAVE")

Ph.D. Graduate Student, Biomechanics: Mr. Sanjiv Parikh

Project Description

Molecular docking, the process by which two or more molecules recognize and interact with one another, is a crucial event in biochemistry. For example, it is central to many fundamental regulatory processes in cells, and it is the basis for practical applications such as drug design and protein engineering. Major challenges in this field are (1) predicting how molecules will dock with one another and (2) identifying the factors that determine the specificity of interaction.

Several approaches to molecular docking have been developed, all of which rely on the number-crunching capabiliities of computers to generate and evaluate large numbers of possible binding orientations. However, they do not take advantage of the graphical capabilities offered by computers. Moreover, existing methods purportedly enhance objectivity by limiting human intervention, but in so doing they severely limit the scientist's ability to analyze the solutions that are provided and exploit their chemical intuition, expertise, and experience in generating a sound and reliable solution. To make major advances in molecular docking, it is necessary to develop novel methods to facilitate the docking techniques by enhancing our ability to understand and analyze docking interactions and to develop hypotheses about which molecules are most likely to interact favorably. These factors can be incorporated into molecular docking by including visualization and haptic (sense of touch) feedback in the process. With this funding from ASPIRES, we will combine visualization and haptic feedback to study molecular docking on workstations, and Immersadesk, and a completely immersive environment, the CAVE. As a result, we will have at our disposal a state-of-the-art research tool that is not available at most other institutions, thereby increasing our competitive advantage for external funding.

Specific Objectives

  1. To implement haptic feedback for interactive molecular docking on graphics workstations and in the CAVE.
  2. To evaluate the effectiveness of interactive docking by comparing the results of docking simulations with experimental data.
  3. To perform docking simulations, the results of which will support current research as well as provide preliminary data for grant applications.
  4. To evaluate the ease of use of interactive molecular docking.
Progress (March 17, 2001): PHANToM <-> VRPN <-> DIVERSE link between Windows PCs and Linux workstations, shown in Figure 2, has been successfully demonstrated. The next step is to include the CAVE and IDesk with DIVERSE. Expected completion date May 2001.

Progress (August 28, 2001): Final report (NISTreport.doc) and associated code can be downloaded from NIST_phaseII



Figure 1. NCSA IDock Project, http://www.ncsa.uiuc.edu/Vis/Projects/Docker



Figure 2. IDock Device Independent Virtual Environemnt.


Select this link for large image of poster

Figure 3. Poster presentation at the Virginia Tech Bioinformatics Conference, March, 19, 2001.


Please contact David Bevan at drbevan@vt.edu or Ron Kriz at: rkriz@vt.edu for more information
Last Revision March 15, 2001
http://www.sv.vt.edu/future/cave/resprj/idock/idock.html