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Department of Chemistry & Biochemistry
The University of Texas at Austin
1 University Station A5300
Austin, TX 78712-0165
Contact Information
Office: ACE: 4.422
Phone: 232-5415
Lab
Office:
Phone:
Fax:
Ron Elber
ron@ices.utexas.edu
Professor W.A. 'Tex' Moncrief Chair in Computational Life Sciences
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Research GroupDr. Elber's Research Group |
EducationBachelor of Science, Hebrew University, 1981 Ph.D., Hebrew University, 1984 |
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AwardsAmerican 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 |
Affiliations
Institute for Computational and Engineering Sciences; Academic Director: Molecular Biophysics Portfolio Program;
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
Krzysztof Kuczera, Gouri Jas, and Ron Elber "The kinetics of helix unfolding: Molecular dynamics simulations with Milestoning" Journal of Physical Chemistry A. 113 (2009): 7461-7473.
Vallat Brinda, Pillardy Jaroslaw, Majek Peter, Meller Jaroslaw, Blom Thomas, Cao Baoqiang, Ron Elber "Building and assessing atomic models of proteins from structural templates: Learning and benchmarks" Proteins, Structure, Function and Bioinformatics 76 (2009): 930-945.
Májek Peter and Elber Ron "A coarse grained potential for fold recognition and molecular dynamics simulations of proteins" Proteins, Structure, Function and Bioinformatics 76 (2009): 822-836.
Steinberg M.Z., Elber, R., McLafferty F.W., Gerber R.B., Breuker, K. "Early Structural Evolution of Native Cytochrome c after Solvent Removal" Chem. Bio. Chem. 9 (2008): 2417-2423.
Vanden-Eijnden Eric, Maddalena Venturoli, Giovanni Ciccotti, and Ron Elber "On the assumptions underlying Milestoning" J. Chem. Phys. 129 (2008): 274102.