Publications

An asterisk (*) indicates a publication with J. Baudry as Corresponding Author:

Published since independent position (2008) - from most recent



79. Ensemble Docking in Drug Discovery: How Many Protein Configurations from Molecular Dynamics Simulations Are Needed to Reproduce Known Ligand Binding?

W Evangelista, SR Ellingson, JC Smith, JY Baudry

J. Phys. Chem B. 2019 Jun 27;123(25):5189-5195

78. Small molecule condensin inhibitors

H Zhao, ZM Petrushenko, JK Walker, J Baudry, HI Zgurskaya, W Rybenkov

ACS infectious diseases 4 (12), 1737-1745

R E Amaro, J Baudry, J Chodera, Ö Demir, J A McCammon, Y Miao, J C Smith

Volume 114, Issue 10, 22 May 2018, Pages 2271-2278

76. Computationally identified novel agonists for GPRC6A

M Pi, K Kapoor, R Ye, DJ Hwang, DD Miller, JC Smith, J Baudry, LD Quarles

PloS one 13 (4), e0195980 2018

75. GPCR6A is a Molecular Target for the Natural Products Gallate and EGCG in Green Tea

M Pi, K Kapoor, R Ye, JC Smith, J Baudry, LD Quarles

Molecular nutrition & food research 2018

74. Ensemble docking to difficult targets in early‐stage drug discovery: Methodology and application to fibroblast growth factor 23

HA Velazquez, D Riccardi, Z Xiao, LD Quarles, CR Yates, J Baudry, JC Smith

Chemical biology & drug design 91 (2), 2018, 491-504

73. Polycystin-1 interacts with TAZ to stimulate osteoblastogenesis and inhibit adipogenesis

Z Xiao, J Baudry, L Cao, J Huang, H Chen, CR Yates, W Li, B Dong, CM Waters, JC Smith, LD Quarles

The Journal of clinical investigation 128 (1), 2018, 157-174

72. Binding Mechanisms of Electron Transport Proteins with Cyanobacterial Photosystem I: An Integrated Computational and Experimental Model

K Kapoor, DJ Cashman, L Nientimp, BD Bruce, J Baudry

J. Phys. Chem. B, 2018, 122 (3), 2017, 1026–1036,

71. Novel Small Molecule JP-153 Targets the Src-FAK-Paxillin Signaling Complex to Inhibit VEGF-Induced Retinal Angiogenesis (vol 91, pg 1, 2017)

JJ Toutounchian, J Pagadala, DD Miller, J Baudry, F Park, E Chaum, V Morales-Tirado, CR Yates

MOLECULAR PHARMACOLOGY 92 (6), 2017, 627-627

70. The quinic acid derivative KZ-41 prevents glucose-induced caspase-3 activation in retinal endothelial cells through an IGF-1 receptor dependent mechanism

H He, RL Weir, JJ Toutounchian, J Pagadala, JJ Steinle, J Baudry, DD Miller, CR Yates

PloS one 12 (8), 2017, e0180808

69. Thermophilic Enzyme or Mesophilic Enzyme with Enhanced Thermostability: Can We Draw a Line?

X Jing, W Evangelista Falcon, J Baudry, EH Serpersu

The Journal of Physical Chemistry B 121 (29), 2017, 7086-7094

68. Identification and Structure–Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli

KM Haynes, N Abdali, V Jhawar, HI Zgurskaya, JM Parks, AT Green, J Baudry, VV Rybenkov, JC Smith, JK Walker

Journal of Medicinal Chemistry 60 (14), 2017, 6205-6219

67. Structure-based design of broadly protective group a streptococcal M protein-based vaccines

JB Dale, PR Smeesters, HS Courtney, TA Penfound, CM Hohn, JC Smith, J Baudry

Vaccine 35 (1), 2017, 19-26

66. Novel small molecule JP-153 targets the Src-FAK-paxillin signaling complex to inhibit VEGF-induced retinal angiogenesis

JJ Toutounchian, J Pagadala, DD Miller, J Baudry, F Park, E Chaum, CR Yates

Molecular pharmacology 91 (1), 2017, 1-13

65. Targeting Src/FAK/Paxillin Signalsome in Neovascular Disease

Jordan J. Toutounchian, Jayaprakash Pagadala, Duane D. Miller, Jerome Baudry, Frank Park, Edward Chaum and Charles R. Yates

Molecular Pharmacology January 1, 2017, 91 (1) 1-13;

64., Structure-based design of broadly protective group a streptococcal M protein-based vaccines

James B. Dale, Pierre R. Smeesters, Harry S. Courtney, Thomas A. Penfound, Claudia M. Hohn, Jeremy C. Smith, Jerome Y. Baudry

Vaccine, Volume 35, Issue 1, 2017, Pages 19-26, ISSN 0264-410X,.

63. A computationally identified compound antagonizes excess FGF-23 signaling in renal tubules and a mouse model of hypophosphatemia

By Zhousheng Xiao, Demian Riccardi, Hector A. Velazquez, Ai L. Chin, Charles R. Yates, Jesse D. Carrick, Jeremy C. Smith, Jerome Baudry, L. Darryl Quarles.

Sci. Signal.22 Nov 2016 : ra113

62. Reviving Antibiotics: Efflux Pump Inhibitors That Interact with AcrA, a Membrane Fusion Protein of the AcrAB-TolC Multidrug Efflux Pump

Narges Abdali, Jerry M. Parks, Keith M. Haynes, Julie L. Chaney, Adam T. Green, David Wolloscheck, John K. Walker, Valentin V. Rybenkov, Jerome Baudry, Jeremy C. Smith, and Helen I. Zgurskaya

ACS Infectious Diseases

DOI: 10.1021/acsinfecdis.6b00167

61. (*) Highly Dynamic Anion–Quadrupole Networks in Proteins

Karan Kapoor, Michael R. Duff, Amit Upadhyay, Joel C. Bucci, Arnold M. Saxton, Robert J. Hinde, Elizabeth E. Howell, and Jerome Baudry

Biochemistry 2016 55 (43), 6056-6069

DOI: 10.1021/acs.biochem.6b00624

60. (*) Ensemble-based docking: From hit discovery to metabolism and toxicity predictions

W Evangelista, RL Weir, SR Ellingson, JB Harris, K Kapoor, JC Smith, and J. Baudry

In Press. Bioorganic & Medicinal Chemistry (2016)

(Baudry co-corresponding author with Smith)

59. Evidence for Osteocalcin Binding and Activation of GPRC6A in β-Cells

M Pi, K Kapoor, R Ye, SK Nishimoto, JC Smith, J Baudry, LD Quarles

Endocrinology (2016) 157 (5), 1866-1880

58. (*) Discovery of Novel Non-Active Site Inhibitors of the Prothrombinase Enzyme Complex

K. Kapoor, N. McGill, C. Peterson, H. Meyers, M. Blackburn and J. Baudry

J. Chem. Inf. Model. (2016) 56 (3), 535-547

(Baudry co-corresponding author with Blackburn)

57. General Trends of Dihedral Conformational Transitions in a Globular Protein

Y. Miao, J. Baudry, JC. Smith and A. McCammon

PROTEINS: Structure, Function, and Bioinformatics (2016) DOI: 10.1002/prot.24996

M Pi, K Kapoor, Y Wu, R Ye, SE Senogles, SK Nishimoto, DJ Hwang, DD Miller, R Narayanan, JC Smith, J. Baudry, and LD Quarles

Molecular Endocrinology (2015) 29 (12), 1759-1773

55. (*) Discovery of an Inhibitor of Z-Alpha 1 Antitrypsin Polymerization

V. Berthelier, J.B. Harris, K.N. Estenson, and J. Baudry

PLOS ONE (2015) 10.1371/journal.pone.0126256

(Baudry co-corresponding author with Berthelier)

54. Multi-Conformer Ensemble Docking to Difficult Protein Targets

S Ellingson, Y. Miao, J. Baudry and J.C. Smith

J. Phys. Chem. B. (2014), DOI: 10.1021/jp506511p

53. (*) 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 (10), 597-608.

(Baudry co- corresponding author with Bruce)

52. (*) 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.

(Baudry co- corresponding author with Layton)

51. (*) Polypharmacology and Supercomputer-Based Docking: Opportunities and Challenges

S. Ellingson, J.C. Smith, and J. Baudry

Molecular Simulation, (2014) DOI: 10.1080/08927022.2014.899699

(Baudry corresponding author)

50. (*) 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, DOI:10.1038/ncomms3881

(Baudry co-corresponding author with Zhulin)

49. 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), DOI: 10.1371/journal.pcbi.1003337

48. (*) Homology Modeling of the CheW Coupling Protein of the Chemotaxis Signaling Complex

D. Cashman, D. Ortega., I. Zhulin., and J. Baudry

PLOS One 8(8): e70705. doi:10.1371/journal.pone.0070705

(Baudry corresponding author)

47. (*) VinaMPI: Facilitating Multiple Receptor High-Throughput Virtual Docking on High Performance Computers

S. Ellingson, J.C. Smith, and J. Baudry

J. Comput. Chem. (2013) DOI: 10.1002/jcc.23367

(Baudry corresponding author)

SR Ellingson, S Dakshanamurthy, M Brown, JC Smith, and J Baudry.

Concurrency and Computation: Practice and Experience. (2013) DOI:10.1002/cpe.3070

(Baudry corresponding author)

D. C. Glass, M. Krishnan, J. C. Smith, J. Baudry

J. Phys. Chem. B. (2013), 117 (11): 3127-3134

(Baudry corresponding author)

44. (*) 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

(Baudry corresponding author)

43. 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

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

41. (*) 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

ECMLS 2012,

(Baudry corresponding author)

40. (*) High-Throughput Virtual Molecular Docking with AutoDockCloud

S.R. Ellingson and J. Baudry

Concurrency and Computation: Practice and Experience.2012 doi: 10.1002/cpe.2926

(Baudry corresponding author)

Z. Yi, Y. Miao, J. Baudry, N. Jain, and J. C. Smith

J. Phys. Chem. B. (2012),116 (16): 5028–5036

38. (*) 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

(Baudry co-corresponding author)

37. 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) EPub ahead of print. PMID:22183804

36. (*) Active site hydration and water diffusion in cytochrome P450cam: a highly dynamic process.

Y. Miao and J. Baudry

Biophysical Journal, (2011), 101 (6): 1493-1503

(Baudry corresponding author)

35. Arabidopsis 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, C. Won-Gyu, I. Wallace, J. Baudry, and D. Roberts

Biochemistry, (2011), 50(31): 6633–6641

34. (*) Three-dimensional mapping of micro-environmental control of methyl rotational barriers.

W.I. Hembree and J. Baudry

J. Phys. Chem. B. (2011), 115 (26): 8575–8580

(Baudry corresponding author)

33. (*) High-Throughput Virtual Molecular Docking: Hadoop Implementation of AutoDock4 on a Private Cloud.

S.R. Ellingson and J. Baudry

ECMLS 2011

(Baudry corresponding author)

32. A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-π pairs.

V. Phillips, J. Harris, R, Adams, D. Nguyen, J. Spiers, J. Baudry, E.E. Howell and R.J. Hinde

Biochemistry, (2011) 50 (14):2939-2950

31. (*)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

J. Comput. Chem. (2011) 32 (6): 1202–1209

(Baudry corresponding author)

Published based on work done before independent position: 30 publications, 14 with Baudry first author, 4 with Baudry corresponding author.

30 other publications

Selected publications amongst the 30 pre-independent papers:

Biasing reaction pathways with mechanical force

CR Hickenboth, JS Moore, SR White, NR Sottos, J Baudry, SR Wilson

Nature 446 (7134), 423-427 (2007)

(*) Van der Waals interactions and decrease of the rotational barrier of methyl-sized rotators: a theoretical study

J Baudry

Journal of the American Chemical Society 128 (34), 11088-11093 (2006)

Determinants of catalytic power and ligand binding in glutamate racemase

MA Spies, JG Reese, D Dodd, KL Pankow, SR Blanke, J Baudry

Journal of the American Chemical Society 131 (14), 5274-5284 (2008)

(*) Can proteins and crystals self-catalyze methyl rotations?

J Baudry, JC Smith

The Journal of Physical Chemistry B 109 (43), 20572-20578 (2005)

(*)Structure-Based Design and In Silico Virtual Screening of Combinatorial Libraries. A Combined Chemical-Computational Project

J Baudry, PJ Hergenrother

J. Chem. Educ 82 (6), 890 (2005)