SAPAC VisLab, using Chimera

DNA, represented using Chimera

Interactive stereo visualisation of modelled molecular structures

Dr. Grant Booker, School of Molecular and Biomedical Science, University Of Adelaide

Using molecular visualisation software such as Chimera, SAPAC's VisLab and SAVRC allow researchers to view molecules with full stereoscopic vision. This allows their three-dimensional structures to be interpreted much more readily than is the case with non-stereo imagery. This is particularly important when the interaction between molecules is of concern, since this is related to how closely the different molecules' surfaces can come into contact.

The ability to see directly this level of contact allows researchers to classify and rank molecular models very rapidly, thus greatly enhancing the efficiency of the molecular modelling process.

From Dr. Booker: "We have been using the VisLab to review protein structures that have been determined either locally or with colleagues from interstate and overseas. The ability to discuss the details of the three-dimensional structures with others helps to make sense of the molecular mechanisms associated with the functions of these proteins.

"Using the Vis Lab, we review the results of molecular docking experiments. We screen a target protein structure with the 3D coordinates of structures of up to 500,000 organic compounds using Dock 5.0 from the UCSF. A consensus-scoring algorithm is then used to select candidate structures that may act as ligands for the target. As a group, we are able to decide which of the top 50 candidates meet a range of criteria such as how well the shape of the molecule complements the binding site.

"We then purchase those compounds that meet our criteria for testing in biochemical or biological assays. Using this process we have been able to find high-affinity enzyme inhibitors.

"We have also been using SAVRC for Biochemistry III tutorials in order better to explain the intricacies of protein structure to students."