Chemical interactions through force feedback

In the Chemical Force Feedback (CFF) system developed at NVIS, Linköping University, the forces between a protein and a substrate can be examined in real-time, giving both visual and haptic feedback. This is done by extracting gradient information from pre-calculated potential fields based on a protein, thus evaluating the forces acting on the substrate virtually held by the user.

Computational Chemistry provides a method for the analysis of chemical systems and reactions through computational simulation and allows chemists to study interactions which cannot be examined using experimental methods. Of particular interest are the studies targeted at the development of new drugs, aiding in the treatment of several medical disorders. The processes within the human body often involve large proteins interacting with smaller molecules in docking procedures; a substrate molecule enters an active site on the protein and connects with it through a set of bonds.

The potential fields currently used are generated by AutoGrid and are based on a protein structure. AutoGrid is a part of the AutoDock package, normally used to simulate the docking process through advanced genetic algorithms. As long as the potential fields are generated with sufficient support with respect to the substrate’s atom types, any substrate can be tested against the protein.

Using a haptic display the user of the CFF system can hold on to a substrate molecule, move it around and feel its interaction with the surrounding atoms of the protein. Being able to feel that which cannot be seen, or being given an extra emphasis to a visual cue, can give a gain in the amount of information perceived by the user. This can lead to a greater understanding of molecular structures and may help scientists all over the world in their research in the area of molecular interactions, such as those involved in drug design.

The application has potential to become a very useful tool for both students and scientists, as it can aid the understanding of molecules at multiple levels. A student who is not familiar with the strong forces involved in a docking procedure can gain insight into the basic molecular interactions and a scientist might realize just what it is that influences the outcome of an experiment.

Although the application is not expected to replace the automated simulations of docking procedures, it is considered to have great potential both for computational steering and result verification, combining the knowledge and intuition of humans with the efficiency of machine calculations.