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.
147. Serdal Kirmizialtin and Ron Elber, “Molecular Machines”, Current Opinion in Structural Biology 23,206-211(2013)
146. Shruthi Viswanath, D. V. S. Ravikant, and Ron Elber, “Improving ranking of models for protein complexes with side chain reconstruction and atomic potentials”, Proteins, Structure, Function and Bioinformatics, 81,592-606(2013).
145. A Peter Ruymgaart and Ron Elber, “Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE Parallelization”, Journal of Chemical Theory and Computations, 8,4624-4636(2012).
144. Mauro Mugnai and Ron Elber, “Thermodynamic Cycle Without Turning Off Self-Interactions: Formal Discussion and a Numerical Example”, Journal of Chemical Theory and Computations, 8,3022-3033(2012).