Jerome Baudry

Assistant Professor - Department of Biochemistry and Cellular and Molecular Biology

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Dr. Jerome Baudry obtained his Ph.D. in Molecular Biophysics with the Highest Honors from the University of Paris, France (University Pierre and Marie Curie), He subsequently joined the group of Klaus Schulten at the University of Illinois at Urbana-Champaign as a post-doc. After his post-doctoral work, Dr. Baudry worked in the pharmaceutical industry as a Research Scientist, and then accepted a Research Assistant Professor position in the School of Chemical Sciences at the University of Illinois, Urbana-Champaign. Dr. Baudry joined the University of Tennessee, Knoxville as a tenure-track faculty  in the Department of Biochemistry & Cell and Molecular Biology. Dr Baudry holds a Group Leader position in the UT/ORNL Center for Molecular Biophysics located on the ORNL campus, and a faculty position in the UT Institute of Biomedical Engineering. The Baudry laboratory develops and applies methods and protocols in computational molecular biophysics for structure-based molecular discovery. The lab works on several targets relevant to human and animal health as well as on targets of agrochemical interest. The theoretical approach is complemented by close collaborations with experimental groups. The Baudry lab is pursuing directed protein engineering projects to design biomolecules with novel and/or directed biological functions.

Research Areas: Molecular Modeling and Computational Molecular Biophysics of Protein/Ligand Interactions and of Protein Structure/Function Relationship

Skills and Expertise: Biophysics | Computational Biology | Molecular Biophysics | Drug Design | Supercomputing

Selected Publications:

Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex
D. Cashman, D. Ortega., I. Zhulin, and J. Baudry, PLOS One , vol. 8, no. 8, pp. e70705, 2013.
VinaMPI: Facilitating Multiple Receptor High-Throughput Virtual Docking on High Performance Computers
S. Ellingson, J.C. Smith, and J. Baudry, Journal of Computational Chemistry, doi: 10.1002/jcc.23367, 2013.
Accelerating Virtual High‐throughput Ligand Docking: Current Technology and Case Study on a Petascale Supercomputer
S.R. Ellingson, S. Dakshanamurthy, M. Brown, J.C. Smith, and J. Baudry, Concurrency and Computation: Practice and Experience, I: 10.1002/cpe.3070, 2013.
Three Entropic Classes of Side Chains in a Globular Protein
D. C. Glass, M. Krishnan, J. C. Smith, J. Baudry, The Journal of Physical Chemistry B, vol. 117, no. 11, pp. 3127-3134, 2013.
STAAR: Statistical Analysis of Aromatic Rings
D.D. Jenkins, J.B. Harris, E.E. Howell, R.J. Hinde, J. Baudry, Journal of Computational Chemistry, vol. 34, no. 6, pp. 518-22, 2013.
High-Throughput Virtual Molecular Docking with AutoDockCloud
S.R. Ellingson and J. Baudry, Concurrency and Computation: Practice and Experience, DOI: 10.1002/cpe.2926, 2012.
Task-parallel Message Passing Interface Implementation of Autodock4 for Docking of Very Large Databases of Compounds Using High-performance Super-computers
B. Collignon, R. Schulz, J.C. Smith, and J. Baudry, Journal of Computational Chemistryf, vol. 32, no. 6, pp. 1202-1209, 2011.
Active-site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process
Y. Miao and J. Baudry, Biophysical Journal, vol. 101, no. 6, pp. 1493-1503, 2011.
Biasing Reaction Pathways with Mechanical Force
C.R. Hickenboth, J.S. Moore, S.R. White, N.R. Sottos, J. Baudry, and S.R. Wilson, Nature, vol. 446, no. 423-427, 2007.
Van der Waals Interactions and Decrease of the Rotational Barrier of Methyl-size Rotators: A Theoretical Study
J. Baudry, Journal of the American Chemical Society, vol. 128, no. 34, pp. 11088-11093, 2006.