Ron Elber

ron@ices.utexas.edu
Physical Chemistry
Professor, Faculty
W.A. "Tex" Moncrief Chair in Computational Life Sciences and Biology
Ron Elber

Contact Information

Office
ACE 4.422
Office Phone
232-5415

Education

Bachelor of Science, Hebrew University (1981);   Ph.D., Hebrew University (1984)

Awards

Alon Fellow (1994, 1993, 1992);   Bergman Award (1993);   Camille and Henry Dreyfus New Faculty (1992, 1991, 1990, 1989, 1988, 1987);   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.

Representative Publications

  • Leonid Meyerguz, Jon Kleinberg, and Ron Elber  "The network of sequence flow between protein structures" Proc. Natl. Acad. Sci. USA 104 (2007): 11627-11623.

  • Chun-Nam John Yu, Thorsten Joachims, Ron Elber and Jaroslaw Pillardy  "Support Vector Training of Protein Alignment Models" RECOMB (2007)

  • Ron Elber  "A milestoning study of the kinetics of an allosteric transition: Atomically detailed simulations of deoxy Scapharca hemoglobin" Biophysical J. 92 (2007): L85-L87.

  • Anthony M.A. West, Ron Elber, and David Shalloway  "Extending molecular dynamics timescales with milestoning: Example of complex kinetics in a solvated peptide" J. Chem. Phys. 126 (2007): 145104.

  • Ron Elber  "Calculations of classical trajectories with boundary value formulation" Lecture Notes in Physics 703 (2006): 435-451.