Contact InformationOffice: ACE: 4.422
Professor W.A. ‘Tex’ Moncrief Chair in Computational Life Sciences
Bachelor of Science, Hebrew University, 1981
Ph.D., Hebrew University, 1984
American Physical Society Fellow, 2009
Alon Fellow, 1994
Bergman Award, 1993
Camille and Henry Dreyfus New Faculty, 1992
University of Illinois Fellow, 1991
Stein Award, 1984
Modeling proteins with biophysics and bioinformatics
On the biophysics front we are interested in computational algorithms to extend the time scale of simulations in molecular biophysics. Straightforward simulation techniques allow the exploration of nanosecond processes. This is much shorter than the microsecond and millisecond time scales of protein folding, channel activation, and allosteric transitions of proteins. All are critical processes of living cells. We develop methods for global optimization of approximate trajectories and pathways for qualitative analysis of long-time mechanisms in molecular biophysics. Recently we also developed a quantitative non-Markovian theory (milestoning) that extracts information from short-time dynamics and allows the calculation of long-time biologically relevant processes. Our ideas, theories, and algorithms are summarized in the software package MOIL. On the bioinformatics front we develop machine-learning approaches to model protein structures from sequences (summarized in our web server LOOPP). We also use these techniques to investigate the network of sequence flow between protein structures and propose a novel picture of protein space that suggests sequence migration between distinct three dimensional shapes, a finding with significant relevance to protein design and evolution.
129. Serdal Kirmizialtin and Ron Elber, “Revisiting and Computing Reaction Coordinates with Directional Milestoning”, J. Phys. Chem. A, 115,6137-6148(2011).
128 Ron Elber, “Simulations of Allosteric Transitions”, Current Opinion in Structural Biology, 21,167-172(2011)
125 Peter Májek and Ron Elber, “Milestoning without a reaction coordinate”, Journal of Chemical Theory and Computations 6,1805–1817(2010).
124 Ron Elber, “Ligand diffusion in globins: Simulations versus experiments”, Current Opinion in Structural Biology, 20,162-167(2010)
123 Ron Elber and Anthony West, “Atomically Detailed Simulation of the Recovery Stroke in Myosin by Milestoning”, Proceeding of the National Academy of Sciences USA, 107, 5001-5005 (2010)