Computational Bionanosensor Design

We have recently started a project entitled, “A Generalized Computational Methodology for the Design of Genetically Encoded Fluorescent Biosensors” with professors Emrah Eroğlu and Ali Rana Atılgan. The project aims to develop a holistic process that eliminates experimental trial and error stages in biosensor design, takes into account not only the binding region but rather the whole protein structure, and therefore puts more emphasis on the computational steps while also including experimental measurements. For details, please see the related GazeteSU article [1].
 
As a side project, we wish to look into strengthening the ammonium binding properties of a potassium probe developed experimentally in the Emrah Eroglu lab. For this purpose, we will use computational biology tools to model the related protein, explore its binding site properties, compare it with other potassium and ammonium probes and suggest point mutations to achieve stong binding to the latter. Our main computational tool will be the VMD/NAMD suite of programs [2, 3].
 
[1] https://gazetesu.sabanciuniv.edu/node/9854
[2] https://www.ks.uiuc.edu/Research/vmd/
[3] http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html