Jerome Baudry, Ph.D.

Publication List – March 2007

Patent Applications:

Probes, Systems and Methods for Drug Discovery

A.M.M. Mjalli, C.Y. Wysong, J. Baudry, T.S. Yokum, R. Andrews and W.K. Banner.

US and International Patent, Assignee: Transtech Pharma, Inc., Application number: 20030125315.

Systems and Methods for Computer-Aided Molecular Discovery

R.I. Sawafta, J. Baudry M.E. Kutz and G. Subramanian.

US and International Patent,Assignee: Transtech Pharma, Inc., Application Number: 20040019432.

Peer-Reviewed Publications (From Most Recent):

(*): Indicates Papers With Jerome Baudry As Corresponding Author

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26. 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 (2007) 446:423-427

[SEE Nature. COVER]

25. (*) 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

24. 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

[SEE Prot. Eng. Des. Sel. COVER]

23. (*) Can Proteins and Crystals Self-Catalyze Methyl Rotations?

J. Baudry and J.C. Smith

J. Phys. Chem. B. (2005) 109: 20572-20578

22. (*) 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

21. 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

20. 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

[SEE Arch. Biochem. Biophys. COVER]

19. (*) Complementarities and Convergence of Results in Bacteriorhodopsin Trimer Simulations.

J. Baudry, E. Tajkhorshid and K. Schulten

Biophys. J. (2004) 87:1394-1395

18. Classical Force Field Parameters for the Heme Prosthetic Group of Cytochrome C.

F. Autenrieth, E. Tajkhorshid, J. Baudry, and Z. Luthey-Schulten

J. Comp. Chem. (2004) 25(13):1613-1622

17. Structural and Functional Evolution of Insect CYP6B Proteins: From Specialist to Generalist P450.

X. Li., J. Baudry, M.R. Berenbaum and M. A. Schuler

Proc. Natl. Acad. Sci. USA. (2004) 101(9):2939-2944

16. Identification of Variable Amino Acids in the SRS1 Region of CYP6B1 Modulating Furanocoumarin Metabolism.

L. Pan, Z. Wen, J. Baudry, M.R. Berenbaum and M.A. Schuler

Arch. Biochem. Biophys. (2004) 422(1):31-41

15. Common Active Site Architecture and Binding Strategy of Four Phenylpropanoid P450s from Arabidopsis Thaliana as Revealed by Molecular Modeling.

S. Rupasinghe, J. Baudry and M. A. Schuler

Protein Engineering (2003) 16:721-731

14. Molecular Docking of Substrates and Inhibitors in the Catalytic Site of CYP6B1, an Insect Cytochrome P450 Monooxygenase.

J. Baudry, W. Li, L. Pan, M.R. Berenbaum and M. A. Schuler

Protein Engineering (2003) 16(8):577-587

13. A-beta, Aging, and Alzheimer’s Disease: A Tale, Models, and Hypotheses.

M.O. Chaney, J. Baudry, C. Esh, J. Childress, D.C. Luehrs, T.A. Kokjohn and A.E. Roher

Neurol. Res., (2003) 25(6):581-590

12. Molecular Basis for the Subtype Discrimination of the Estrogen Receptor Beta Selective Ligand, Diarylpropionitrile.

J. Sun, J. Baudry, J.A. Katzenellenbogen, and B.S. Katzenellenbogen

Mol. Endocrinol. (2003) 17(2):247-258

11. Steered Molecular Dynamics Investigations of Protein Function.

B. Isralewitz, J. Baudry, J. Gullingsrud, D. Kosztin, and K. Schulten

Journal of Molecular Graphics and Modeling, (2001) 19:13-25

10. Molecular Dynamics Study of Bacteriorhodopsin and the Purple Membrane.

J. Baudry, E. Tajkhorshid, F. Molnar, J. Phillips and K. Schulten

J. Phys. Chem. B. Feature Article (2001) 105(5):905-918

[SEE J. Phys. Chem. B. COVER]

9. Oligomerization and Fibril Assembly of the Amyloid-Beta Protein.

A.E. Roher, J. Baudry, M.O. Chaney, Y.M. Kuo and M.R. Emmerling

Biochemica et Biophysica Acta - Molecular Basis of Disease, (2000) 1502 (1):31-43

8. From Sequence to Structure and Function: Modelling and Simulation of Light-Activated Membrane Proteins.

J. Baudry, S. Crouzy, B. Roux and J.C. Smith

Genomics and Proteomics- Functional and Computational Aspects. S. Suhai (Ed), Kluwer Academic/Plenum Publishers N.Y. (2000) 141-147

7. Molecular Dynamics Study of the Nature and Origin of the Twisted Structure of the Retinal Chromophore In Bacteriorhodopsin.

E. Tajkhorshid, J. Baudry, K. Schulten and S. Suhai

Biophys. J. (2000) 78:683-693

6. Efficient Calculation of 2-Dimensional Adiabatic and Free Energy Maps: Application to the Isomerization of the C13=C14 and C15=N16 Bonds in the Retinal of Bacteriorhodopsin.

S. Crouzy, J. Baudry, J.C. Smith and B. Roux

J. Comp. Chem. (1999) 20:644-1658

5. Simulation Analysis of the Retinal Conformational Equilibrium in Dark-Adapted Bacteriorhodopsin.

J. Baudry, S. Crouzy, B. Roux and J.C. Smith

Biophys. J. (1999) 76:1909-1917

4. Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics.

J. Baudry, S. Crouzy, B. Roux and J.C. Smith

J. Chem. Info. Comput. Sci. (1997) 37:1018-1024

3. Collective Vibrations in The Crystalline Alanine Dipeptide at Very Low Temperatures.

J. Baudry, R.L. Hayward, H.D. Middendorf and J.C. Smith

J. Mol. Struct. Dyn. (Biological Macromolecular Dynamics). (1997) 49-54

2. Harmonic and Anharmonic Dynamics in Protein and Molecular Crystals.

J.C. Smith, J. Baudry, S. Hery, A. Lamy, A. Micu and M. Souaille

In Nonlinear Physics: Theory and Experiment, Eds. M. Alfini, M. Boiti, L. Martina and F. Pempinelli. World Scientific. (1996) 575-581

1. Molecular Mechanics Analysis of Peptide Group Bonding Cooperativity and Influence on Phi and Psi Barriers.

J. Baudry and J.C. Smith

Journal of Molecular Structure (Theochem) (1994) 308:103-113