DOI: 10.1101/452367Oct 24, 2018Paper

A Novel analog approach for fast evaluation of affinity between ligand and receptor in scaled up molecular models

BioRxiv : the Preprint Server for Biology
Pouya Tavousi, Sina Shahbazmohamadi


Rational structure based drug design aims at identifying ligand molecules that bind to the active site of a target molecule with high affinity (low binding free energy), to promote or inhibit certain biofunctions. Thus, it is absolutely essential that one can evaluate such affinity for the predicted molecular complexes in order to design drugs effectively. A key observation is that, binding affinity is proportional to the geometric fit between the two molecules. Having a way to assess the quality of the fit enables one to rank the quality of potential drug solutions. Other than experimental methods that are associated with excessive time, labor and cost, several in silico methods have been developed in this regard. However, a main challenge of any computation-based method is that, no matter how efficient the technique is, the trade-off between accuracy and speed is inevitable. Therefore, given today's existing computational power, one or both is often compromised. In this paper, we propose a novel analog approach, to address the aforementioned limitation of computation-based algorithms by simply taking advantage of Kirchhoff's circuit laws. Ligand and receptor are represented with 3D printed molecular models that account for th...Continue Reading

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