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Interacting with the biomolecular solvent accessible surface via a haptic feedback device

Matthew B Stocks1, Steven Hayward12 and Stephen D Laycock1*

Author Affiliations

1 School of Computing Sciences, University of East Anglia, Norwich, UK, NR4 7TJ

2 School of Biological Sciences, University of East Anglia, Norwich, UK, NR4 7TJ

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BMC Structural Biology 2009, 9:69  doi:10.1186/1472-6807-9-69

Published: 27 October 2009

Abstract

Background

From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation.

Results

A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations.

Conclusion

By using the software, named HaptiMol ISAS (available from http://www.haptimol.co.uk webcite), one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water accessibility of the biomolecular surface that cannot be so easily attained using conventional molecular graphics software.