Collaborative Tools for Molecular Visualization and Interactive Molecular Dynamics (IMD)


Theoretical Biophysics Group

NIH Resource for Macromolecular Modeling and Bioinformatics

Beckman Institute for Advanced Science and Technology

University of Illinois at Urbana-Champaign



Welcome to the Theoretical Biophysics Group, a UIUC/COE 2001 Open House event. Today we will present two projects simulated by our Molecular Dynamics program NAMD using 3-D stereo graphics produced by our visualization program, VMD. We will also talk about the computational tools we develop and use in our research. For more information go to and


The first project is a simulation study of the regulation of genetic expression in bacteria ( We will show you a model of a repressor protein that shuts down an active DNA site by forcing the DNA to adopt a looped form. The combination of a detailed all-atom model for the protein with a coarse-grained model for the DNA loop helps us to significantly reduce the computational time required to simulate the behavior of this protein-DNA system. Similar models may prove essential for understanding protein machinery in all living cells and even in designing custom proteins for medical use.


Our second project illustrates how through Interactive Molecular Dynamics (IMD) one can manipulate manually, with so-called haptic force feedback, simulated biomolecules for the purpose of drug design ( IMD relies on researchers' sense of touch in their quest to understand how biomolecules work. Via a haptic controller device, IMD applies forces to atoms in running NAMD simulations and displays the results in VMD. We will demonstrate IMD with a simulation of a key process in modern drug discovery, namely the docking of a chemical compound to a protein. Visitors will have the opportunity to experience haptic feedback firsthand.


Finally, we will demonstrate BioCoRE (, a new generation of web-based technology we develop at the Beckman Institute. BioCoRE is a tool-oriented research environment for structural biology within which researchers can visualize information, share resources and interact with each other and with structural biology tools via a common infrastructure and across time zones and continents.


The work of the Theoretical Biophysics Group cuts across disciplines and centers on the structure and function of supramolecular systems in the living cell, and on the development of new algorithms and efficient computing tools for structural biology. Our members come from diverse fields and contribute knowledge from physics, biology, chemistry, computer science, biophysics and even from the behavioral sciences.



Presentation Schedule (sessions are about 25 minutes each):


Friday, March 2: 11 A.M., 1 P.M., 2 P. M., 3 P. M.

Saturday, March 3: 11 A.M., 1 P.M., 2 P.M.