%0 Journal Article
%T Interacting with the biomolecular solvent accessible surface via a haptic feedback device
%A Matthew B Stocks
%A Steven Hayward
%A Stephen D Laycock
%J BMC Structural Biology
%D 2009
%I BioMed Central
%R 10.1186/1472-6807-9-69
%X 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.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.The sense of touch can be used to augment our visual sense to gain a deeper insight into the three dimensional shapes of complex objects. Biomolecules are examples of highly complex three dimensional objects which are often visualised using molecular graphics. Many software programs exist which attempt to convey the three dimensional form of structures utilising stereoscopic viewing methods and depth cues. However, the augmentation of our sense of sight with touch would be a useful aid in understanding the overall three dimensional shape of a biomolecule and in particular the fine surface details that cannot easily be seen whilst visualising the mo
%U http://www.biomedcentral.com/1472-6807/9/69