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Jerome Baudry, Associate Professor
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Jerome Baudry Associate Professor

Department of Biochemistry & Cell and Molecular Biology, University of Tennessee, Knoxville; Center for Molecular Biophysics, Oak Ridge National Laboratory; Institute of Biomedical Engineering, University of Tennessee, Knoxville.


Center for Molecular Biophysics
Building 6011
Oak Ridge National Laboratory

Oak Ridge , Tennessee 37830
Work: (865) 576-0930

Education:

  1. Ph.D. Molecular Biophysics, University of Paris, Pierre and Marie Curie (Paris-06). December 1997.

Biography:

 

J. Baudry Full CV, August 2014 (click here)

 

Professor Jerome Baudry joined the Center for Molecular Biophysics in 2008 as an Assistant Professor at the University of Tennessee, Knoxville; Department of Biochemistry & Cell and Molecular Biology. Dr Baudry obtained his Ph.D. in Molecular Biophysics with the highest Honors from the University of Paris-06, 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 Senior Research Scientist position back in Illinois. Prior to his appointment in Tennessee, Dr. Baudry was Research Assistant Professor in the School of Chemical Sciences at the University of Illinois, Urbana-Champaign.

 

 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 also actively pursues research projects to characterize the role of methyl-rich side chains in the dynamics and the thermodynamics of protein/protein and protein/ligand interactions. This has led the group to further develop frontier projects on the dynamics of satellite functionalization in solid state, and surface-mounted nano rotors.

 

 

RECENT PUBLICATIONS:

Molecular Interactions Between Photosystem I and Ferredoxin: An Integrated Energy Frustration and Experimental Model
D.J. Cashman; T. Zhu; R.F. Simmerman; C. Scott; B.D. Bruce, and J. Baudry
Journal of Molecular Recognition (2014), 27(20):597-608.

A Computational Approach Predicting CYP450 Metabolism and Estrogenic activity of an Endocrine Disrupting Compound (PCB-30)
J.B. Harris, M.L. Eldridge, G. Sayler, F. Menn, A.C. Layton, and J. Baudry
Environmental Toxicology and Chemistry (2014), 33 (7), 1615-1623.

Polypharmacology and Supercomputer-Based Docking: Opportunities and Challenges
S. Ellingson, J.C. Smith, and J. Baudry
Molecular Simulation (2014), 40(10-11):848-854.

A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors.
D. Ortega, C. Yang, P. Ames, J. Baudry, J.S Parkinson, and I. Zhulin
Nature Communications. (2013), 4:2881.

Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein.
D. Ortega, G. Mo., K. Lee, H. Zhou, J. Baudry, D. Dahlquist, and I. Zhulin
PLOS Comp Biol. (2013), 9(11): e1003337.

Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex.
D. Cashman, D. Ortega, I. Zhulin, and J. Baudry
PLOS One (2013), 8(8): e70705.

VinaMPI: Facilitating Multiple Receptor High-Throughput Virtual Docking on High Performance Computers.
S. Ellingson, J.C. Smith, and J. Baudry
Journal of Computational Chemistry (2013), 34(25): 2212–2221

Accelerating Virtual High-Throughput Ligand Docking: Screening One Million Compounds Using a Petascale Supercomputer.
S. Ellingson, S. Dakshanamurthy, M. Brown, J.C. Smith, J. Baudry
Concurrency and Computation: Practice and Experience (2013)

Three Entropic Classes of Side Chains in a Globular Protein.
D. C. Glass, M. Krishnan, J. C. Smith, J. Baudry
J. Phys. Chem. B.  (2013), 117 (11): 3127-3134

STAAR: Statistical analysis of aromatic rings.
D.D. Jenkins, J.B. Harris, E.E. Howell, R.J. Hinde, J. Baudry
J. Comput. Chem. (2013), 34(6): 518-22

Coupled Flexibility Change in Cytochrome P450cam Substrate Binding Determined by Neutron Scattering, NMR, and Molecular Dynamics Simulation.
Y. Miao, Z. Yi, C. Cantrell, D.C. Glass, J. Baudry, N. Jain, J.C. Smith
Biophysical journal (2012), 103 (10): 2167-2176

Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein.
Y. Miao, Z. Yi, D.C. Glass, L. Hong, M. Tyagi, J Baudry, N. Jain, J.C. Smith
J. Am. Chem. Soc. (2012) 134 (48): 19576-19579

High-Throughput Virtual Molecular Docking with AutoDockCloud.
S.R. Ellingson and J. Baudry
Concurrency and Computation: Practice and Experience. doi: 10.1002/cpe.2926

Coenzyme-A Binding to the Aminoglycoside Acetyltransferase (3)-IIIb Increases Conformational Sampling of Antibiotic Binding Site.
X. Hu, A.L. Norris, J. Baudry, and E.H. Serpersu.
Biochemistry (2011) 50(48): 10559-10565

Coenzyme-A Binding to the Aminoglycoside Acetyltransferase (3)-IIIb Increases Conformational Sampling of Antibiotic Binding Site.
X. Hu, A.L. Norris, J. Baudry, and E.H. Serpersu.
Biochemistry (2011) 50(48): 10559-10565

VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy.
M.C. Brothers , A.E. Nesbitt, M.J. Hallock, S.G. Rupasinghe, M. Tang, J. Harris, J. Baudry, M.A. Schuler, and C.M. Rienstra
J. Biomolecular NMR. (2011) 52(1):41-56

Active site hydration and water diffusion in cytochrome P450cam: a highly dynamic process.
Y. Miao and J. Baudry
Biophysical Journal (2011), 101(6):1493-503

High-Throughput Virtual Molecular Docking: Hadoop Implementation of AutoDock4 on a Private Cloud.
S.R. Ellingson and J. Baudry (2011)
ECMLS 2011 Proceedings of the second international workshop on Emerging computational methods for the life sciences.

Three-dimensional mapping of micro-environmental control of methyl rotational barriers.
W.I. Hembree and J. Baudry
J Phys Chem B. (2011), 115(26), 8575-80

Arabidopsis thaliana NIP7;1: An Anther-Specific Boric Acid Transporter of the Aquaporin Superfamily Regulated by an Unusual Tyrosine in Helix 2 of the Transport Pore.
T. Li, WG Choi, I.S. Wallace, J. Baudry, and D. M. Roberts
Biochemistry (2011), 50(31), 6633–6641

A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-pairs.
V. Philip, J. Harris, R, Adams, D. Nguyen, J. Spiers, J. Baudry, E.E. Howell and R.J. Hinde.
Biochemistry (2011), 50(14), 2939-2950

Task-parallel MPI implementation of Autodock4 for docking of very large databases of compounds using High Performance Super-Computers
B. Collignon, R.S. Schultz, J.C. Smith and J. Baudry
J. Comput. Chem. (2011), 32(6), 1202–1209

Human TLRs 10 and 1 Share Common Mechanisms of Innate Immune Sensing but Not Signaling
Y. Guan, D.R.E. Ranoa, S. Jiang,. S.K. Mutha, X. Li, J. Baudry, and R.I. Tapping
Journal Immunol. (2010), 184: 5094–5103

Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase.
A.Spies, J.G. Reese, D. Dodd, K.L. Pankow, S.R. Blanke, and J. Baudry.
J. Am. Chem. Soc. (2009) 15;131(14):5274-84.

Key Role of Active-Site Water Molecules in Bacteriorhodopsin Proton-Transfer Reactions.
A.N. Bondar, J. Baudry, S. Suhai, S. Fischer, and J.C. Smith.
J. Phys. Chem. B. 112, 14729-14741 (2008)

Biasing Reaction Pathways with Mechanical Force.
C. R. Hickenboth, J.S. Moore, S.R. White, N. R. Sottos, J. Baudry
Nature (2007) 446:423-427

van der Waals Interactions and Decrease of the Rotational Barrier of Methyl-size Rotators: A Theoretical Study.
J. Baudry
J. Am. Chem. Soc. (2006) 128(34):11088-11093

Class-Dependent Sequence Alignment Strategy Improves the Structural and Functional Modeling of P450s.
J. Baudry, S. Rupasinghe, and M. Schuler
Protein Eng. Des. Sel. (2006) 19(8):345–353

Can Proteins and Crystals Self-Catalyze Methyl Rotations?
J. Baudry and J.C. Smith
J. Phys. Chem. B. (2005) 109:20572-20578

Structure-based Design and In-Silico Virtual Screening of combinatorial Libraries. A Combined Chemical/Computational Assignment.
J. Baudry and P. Hergenrother
J. Chem. Edu. (2005) 82(6):890-894

Ile115Leu Mutation in the SRS1 Region of an Insect Cytochrome P450 (CYP6B1) Compromises Substrate Turnover via Changes in a Predicted Product Release Channel.Z. Wen, J. Baudry, M.R. Berenbaum, and M.A. Schuler
Protein Eng. Des. Sel. (2005) 18(4):191-199

A Retinoic Acid Binding Cytochrome P450: CYP120A1 from Synechocystis sp. PCC 6803.
N. Ke, J. Baudry, T. Makris, M. A. Schuler and S. G.Sligar
Arch. Biochem. Biophys. (2005) 436:110-120