Dr. Artem Mamonov

Dr. Artem Mamonov

My research interests are in development of new computational techniques for understanding biomolecular phenomena particularly binding and conformational transitions with application to rational drug design. I am currently working on a refinement algorithm for protein-protein structure prediction. Its goal is to complement PIPER — an in-house FFT based docking program. My refinement technique is based on Monte Carlo minimization algorithm complemented by protein side chain repacking and rigid body minimization.

My background is in computational chemistry and molecular biophysics. I have a broad experience working on problems in computational biophysics including modeling ion conductance through narrow biological ion channels, ion channel gating, conformational sampling and free energy calculations in biomolecules. I developed and implemented a library-based Monte Carlo technique for equilibrium sampling of biomolecules which is significantly faster than standard techniques. I also developed and implemented a novel library-based polymer-growth technique for absolute free energy calculation. It can be very useful for calculating binding affinities especially in systems that undergo large conformational transitions. My techniques are used by other researchers for docking and binding affinity calculations.