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Jerome Y. Baudry, Ph.D. - Publications

Affiliations: 
2008-2017 The University of Tennessee, Knoxville, TN, United States 
 2017- Biological Sciences The University of Alabama in Huntsville, Huntsville, AL, United States 
Area:
Drug discovery, supercomputing, virtual screening, molecular modeling, molecular dynamics, computational chemistry
Website:
https://www.uah.edu/science/departments/biology/faculty-staff/jerome-baudry
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76 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Agarwal R, Pattarawat P, Duff MR, Wang HR, Baudry J, Smith JC. Structure-Based Identification of Novel Histone Deacetylase 4 (HDAC4) Inhibitors. Pharmaceuticals (Basel, Switzerland). 17. PMID 39065718 DOI: 10.3390/ph17070867  0.412
2022 Bensing BA, Stubbs HE, Agarwal R, Yamakawa I, Luong K, Solakyildirim K, Yu H, Hadadianpour A, Castro MA, Fialkowski KP, Morrison KM, Wawrzak Z, Chen X, Lebrilla CB, Baudry J, et al. Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation. Nature Communications. 13: 2753. PMID 35585145 DOI: 10.1038/s41467-022-30509-y  0.393
2022 Sripriya Akondi V, Menon V, Baudry J, Whittle J. Novel Big Data-Driven Machine Learning Models for Drug Discovery Application. Molecules (Basel, Switzerland). 27. PMID 35163865 DOI: 10.3390/molecules27030594  0.322
2021 Baudry J, Bondar AN, Cournia Z, Parks JM, Petridis L, Roux B. Editorial: Advances in computational molecular biophysics. Biochimica Et Biophysica Acta. General Subjects. 129888. PMID 33662454 DOI: 10.1016/j.bbagen.2021.129888  0.389
2021 Spencer JA, Penfound T, Salehi S, Aranha MP, Wade LE, Agarwal R, Smith JC, Dale JB, Baudry J. Cross-reactive immunogenicity of group A streptococcal vaccines designed using a recurrent neural network to identify conserved M protein linear epitopes. Vaccine. PMID 33642159 DOI: 10.1016/j.vaccine.2021.01.075  0.351
2020 Kapoor K, Pi M, Nishimoto SK, Quarles LD, Baudry J, Smith JC. The carboxylation status of osteocalcin has important consequences for its structure and dynamics. Biochimica Et Biophysica Acta. General Subjects. 129809. PMID 33340588 DOI: 10.1016/j.bbagen.2020.129809  0.653
2020 Agarwal R, Bensing BA, Mi D, Vinson P, Baudry J, Iverson TM, Smith JC. Structure based virtual screening identifies small molecule effectors for the sialoglycan binding protein Hsa. The Biochemical Journal. PMID 32910185 DOI: 10.1042/Bcj20200332  0.556
2020 Aranha MP, Penfound TA, Spencer JA, Agarwal R, Baudry J, Dale JB, Smith JC. Structure-based group A streptococcal vaccine design: Helical wheel homology predicts antibody cross-reactivity among streptococcal M protein-derived peptides. The Journal of Biological Chemistry. PMID 32029479 DOI: 10.1074/Jbc.Ra119.011258  0.413
2019 Hu X, Smith MD, Humphreys BM, Green AT, Parks JM, Baudry JY, Smith JC. Ligand-Dependent Sodium Ion Dynamics within the A-Adenosine Receptor: A Molecular Dynamics Study. The Journal of Physical Chemistry. B. PMID 31483659 DOI: 10.1021/Acs.Jpcb.9B04474  0.476
2019 Evangelista W, Ellingson SR, Smith JC, Baudry JY. Ensemble Docking in Drug Discovery: How Many Protein Configurations from Molecular Dynamics Simulations Are Needed to Reproduce Known Ligand Binding? The Journal of Physical Chemistry. B. PMID 30695645 DOI: 10.1021/Acs.Jpcb.8B11491  0.77
2018 Zhao H, Petrushenko ZM, Walker JK, Baudry J, Zgurskaya HI, Rybenkov VV. Small Molecule Condensin Inhibitors. Acs Infectious Diseases. PMID 30346684 DOI: 10.1021/Acsinfecdis.8B00222  0.372
2018 Pi M, Kapoor K, Ye R, Hwang DJ, Miller DD, Smith JC, Baudry J, Quarles LD. Computationally identified novel agonists for GPRC6A. Plos One. 13: e0195980. PMID 29684031 DOI: 10.1371/Journal.Pone.0195980  0.691
2018 Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. Ensemble Docking in Drug Discovery. Biophysical Journal. PMID 29606412 DOI: 10.1016/J.Bpj.2018.02.038  0.525
2018 Pi M, Kapoor K, Ye R, Smith JC, Baudry J, Quarles LD. GPCR6A is a Molecular Target for the Natural Products Gallate and EGCG in Green Tea. Molecular Nutrition & Food Research. PMID 29468843 DOI: 10.1002/Mnfr.201700770  0.677
2018 Pi M, Kapoor K, Ye R, Smith JC, Baudry J, Quarles LD. Front cover: GPCR6A Is a Molecular Target for the Natural Products Gallate and EGCG in Green Tea Molecular Nutrition & Food Research. 62: 1870053. DOI: 10.1002/Mnfr.201870053  0.663
2017 Kapoor K, Cashman DJ, Nientimp L, Bruce BD, Baudry JY. Binding Mechanisms of Electron Transport Proteins with Cyanobacterial Photosystem I: An Integrated Computational and Experimental Model. The Journal of Physical Chemistry. B. PMID 29211957 DOI: 10.1021/Acs.Jpcb.7B08307  0.674
2017 Xiao Z, Baudry J, Cao L, Huang J, Chen H, Yates CR, Li W, Dong B, Waters CM, Smith JC, Quarles LD. Polycystin-1 interacts with TAZ to stimulate osteoblastogenesis and inhibit adipogenesis. The Journal of Clinical Investigation. PMID 29202470 DOI: 10.1172/Jci93725  0.45
2017 Velazquez HA, Riccardi D, Xiao Z, Quarles LD, Yates CR, Baudry J, Smith JC. Ensemble Docking to Difficult Targets in Early-Stage Drug Discovery: Methodology and Application to Fibroblast Growth Factor 23. Chemical Biology & Drug Design. PMID 28944571 DOI: 10.1111/Cbdd.13110  0.554
2017 Jing X, Evangelista Falcón W, Baudry JY, Serpersu EH. Thermophilic Enzyme or Mesophilic Enzyme with Enhanced Thermostability: Can We Draw a Line? The Journal of Physical Chemistry. B. PMID 28689415 DOI: 10.1021/Acs.Jpcb.7B04519  0.337
2017 Haynes KM, Abdali N, Jhawar V, Zgurskaya HI, Parks JM, Green AT, Baudry JY, Rybenkov VV, Smith JC, Walker JK. Identification and Structure-Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli. Journal of Medicinal Chemistry. PMID 28650638 DOI: 10.1021/Acs.Jmedchem.7B00453  0.488
2016 Dale JB, Smeesters PR, Courtney HS, Penfound TA, Hohn CM, Smith JC, Baudry JY. Structure-based design of broadly protective group a streptococcal M protein-based vaccines. Vaccine. PMID 27890396 DOI: 10.1016/j.vaccine.2016.11.065  0.359
2016 Xiao Z, Riccardi D, Velazquez HA, Chin AL, Yates CR, Carrick JD, Smith JC, Baudry J, Quarles LD. A computationally identified compound antagonizes excess FGF-23 signaling in renal tubules and a mouse model of hypophosphatemia. Science Signaling. 9: ra113. PMID 27879395 DOI: 10.1126/Scisignal.Aaf5034  0.453
2016 Abdali N, Parks JM, Haynes K, Chaney JL, Green AT, Wolloscheck D, Walker JK, Rybenkov VV, Baudry JY, Smith JC, Zgurskaya HI. Reviving antibiotics: efflux pump inhibitors that interact with AcrA, a membrane fusion protein of the AcrAB-TolC multidrug efflux pump. Acs Infectious Diseases. PMID 27768847 DOI: 10.1021/Acsinfecdis.6B00167  0.443
2016 Kapoor K, Duff MR, Upadhyay A, Bucci JC, Saxton AM, Hinde RJ, Howell EE, Baudry J. Highly Dynamic Anion-Quadrupole Networks in Proteins. Biochemistry. 55: 6056-6069. PMID 27753291 DOI: 10.1021/Acs.Biochem.6B00624  0.666
2016 Evangelista W, Weir RL, Ellingson SR, Harris JB, Kapoor K, Smith JC, Baudry J. Ensemble-based docking: From hit discovery to metabolism and toxicity predictions. Bioorganic & Medicinal Chemistry. PMID 27543390 DOI: 10.1016/J.Bmc.2016.07.064  0.731
2016 Pi M, Kapoor K, Ye R, Kenneth Nishimoto S, Smith JC, Baudry J, Darryl Quarles L. Evidence for Osteocalcin Binding and Activation of GPRC6A in β-Cells. Endocrinology. en20152010. PMID 27007074 DOI: 10.1210/En.2015-2010  0.662
2016 Kapoor K, McGill N, Peterson CB, Meyers HV, Blackburn MN, Baudry JY. Discovery of Novel Non-active Site Inhibitors of the Prothrombinase Enzyme Complex. Journal of Chemical Information and Modeling. PMID 26848511 DOI: 10.1021/Acs.Jcim.5B00596  0.684
2016 Miao Y, Baudry J, Smith JC, McCammon JA. General trends of dihedral conformational transitions in a globular protein. Proteins. 84: 501-14. PMID 26799251 DOI: 10.1002/Prot.24996  0.512
2015 Pi M, Kapoor K, Wu Y, Ye R, Senogles SE, Nishimoto SK, Hwang DJ, Miller DD, Narayanan R, Smith JC, Baudry J, Quarles LD. Structural and Functional Evidence for Testosterone Activation of GPRC6A in Peripheral Tissues. Molecular Endocrinology (Baltimore, Md.). me20151161. PMID 26440882 DOI: 10.1210/Me.2015-1161  0.668
2015 Berthelier V, Harris JB, Estenson KN, Baudry J. Discovery of an inhibitor of Z-alpha1 antitrypsin polymerization. Plos One. 10: e0126256. PMID 25961288 DOI: 10.1371/Journal.Pone.0126256  0.578
2015 Ellingson SR, Miao Y, Baudry J, Smith JC. Multi-conformer ensemble docking to difficult protein targets. The Journal of Physical Chemistry. B. 119: 1026-34. PMID 25198248 DOI: 10.1021/Jp506511P  0.771
2015 Kapoor K, Duff M, Hinde R, Baudry J, Howell E. Characterizing Dynamics of Anion/Pi Interactions through Molecular Dynamics Simulations Biophysical Journal. 108: 379. DOI: 10.1016/J.Bpj.2014.11.2081  0.685
2014 Cashman DJ, Zhu T, Simmerman RF, Scott C, Bruce BD, Baudry J. Molecular interactions between photosystem I and ferredoxin: an integrated energy frustration and experimental model. Journal of Molecular Recognition : Jmr. 27: 597-608. PMID 25178855 DOI: 10.1002/Jmr.2384  0.397
2014 Ellingson SR, Dakshanamurthy S, Brown M, Smith JC, Baudry J. Accelerating Virtual High-Throughput Ligand Docking: current technology and case study on a petascale supercomputer. Concurrency and Computation : Practice & Experience. 26: 1268-1277. PMID 24729746 DOI: 10.1002/Cpe.3070  0.718
2014 Harris JB, Eldridge ML, Sayler G, Menn FM, Layton AC, Baudry J. A computational approach predicting CYP450 metabolism and estrogenic activity of an endocrine disrupting compound (PCB-30). Environmental Toxicology and Chemistry / Setac. 33: 1615-23. PMID 24687371 DOI: 10.1002/Etc.2595  0.558
2014 Ellingson SR, Smith JC, Baudry J. Polypharmacology and supercomputer-based docking: Opportunities and challenges Molecular Simulation. 40: 848-854. DOI: 10.1080/08927022.2014.899699  0.731
2013 Ortega DR, Yang C, Ames P, Baudry J, Parkinson JS, Zhulin IB. A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors. Nature Communications. 4: 2881. PMID 24335957 DOI: 10.1038/Ncomms3881  0.341
2013 Ortega DR, Mo G, Lee K, Zhou H, Baudry J, Dahlquist FW, Zhulin IB. Conformational coupling between receptor and kinase binding sites through a conserved salt bridge in a signaling complex scaffold protein. Plos Computational Biology. 9: e1003337. PMID 24244143 DOI: 10.1371/Journal.Pcbi.1003337  0.381
2013 Cashman DJ, Ortega DR, Zhulin IB, Baudry J. Homology modeling of the CheW coupling protein of the chemotaxis signaling complex. Plos One. 8: e70705. PMID 23950985 DOI: 10.1371/Journal.Pone.0070705  0.374
2013 Ellingson SR, Smith JC, Baudry J. VinaMPI: facilitating multiple receptor high-throughput virtual docking on high-performance computers. Journal of Computational Chemistry. 34: 2212-21. PMID 23813626 DOI: 10.1002/Jcc.23367  0.729
2013 Glass DC, Krishnan M, Smith JC, Baudry J. Three entropic classes of side chain in a globular protein. The Journal of Physical Chemistry. B. 117: 3127-34. PMID 23421556 DOI: 10.1021/Jp400564Q  0.451
2013 Jenkins DD, Harris JB, Howell EE, Hinde RJ, Baudry J. STAAR: statistical analysis of aromatic rings. Journal of Computational Chemistry. 34: 518-22. PMID 23115119 DOI: 10.1002/Jcc.23164  0.568
2013 Li T, Baudry J, Roberts DM. An Unusual Aquaporin-Like Metalloid Boric Acid Channel in Arabidopsis Biophysical Journal. 104: 633a. DOI: 10.1016/J.Bpj.2012.11.3500  0.308
2012 Miao Y, Yi Z, Cantrell C, Glass DC, Baudry J, Jain N, Smith JC. Coupled flexibility change in cytochrome P450cam substrate binding determined by neutron scattering, NMR, and molecular dynamics simulation. Biophysical Journal. 103: 2167-76. PMID 23200050 DOI: 10.1016/J.Bpj.2012.10.013  0.511
2012 Miao Y, Yi Z, Glass DC, Hong L, Tyagi M, Baudry J, Jain N, Smith JC. Temperature-dependent dynamical transitions of different classes of amino acid residue in a globular protein. Journal of the American Chemical Society. 134: 19576-9. PMID 23140218 DOI: 10.1021/Ja3097898  0.467
2012 Yi Z, Miao Y, Baudry J, Jain N, Smith JC. Derivation of mean-square displacements for protein dynamics from elastic incoherent neutron scattering. The Journal of Physical Chemistry. B. 116: 5028-36. PMID 22471396 DOI: 10.1021/Jp2102868  0.476
2012 Brothers MC, Nesbitt AE, Hallock MJ, Rupasinghe SG, Tang M, Harris J, Baudry J, Schuler MA, Rienstra CM. VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy. Journal of Biomolecular Nmr. 52: 41-56. PMID 22183804 DOI: 10.1007/S10858-011-9576-3  0.583
2012 Yi Z, Miao Y, Baudry J, Jain N, Smith JC. Temperature Dependent Dynamics of Cytochrome P450cam from Elastic Incoherent Neutron Scattering Biophysical Journal. 102: 382a. DOI: 10.1016/J.Bpj.2011.11.2089  0.471
2012 Ellingson SR, Baudry J. High-throughput virtual molecular docking with AutoDockCloud Concurrency and Computation: Practice and Experience. 26: 907-916. DOI: 10.1002/Cpe.2926  0.737
2011 Hu X, Norris AL, Baudry J, Serpersu EH. Coenzyme A binding to the aminoglycoside acetyltransferase (3)-IIIb increases conformational sampling of antibiotic binding site. Biochemistry. 50: 10559-65. PMID 22026726 DOI: 10.1021/Bi201008F  0.383
2011 Miao Y, Baudry J. Active-site hydration and water diffusion in cytochrome P450cam: a highly dynamic process. Biophysical Journal. 101: 1493-503. PMID 21943431 DOI: 10.1016/J.Bpj.2011.08.020  0.354
2011 Li T, Choi WG, Wallace IS, Baudry J, Roberts DM. 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. Biochemistry. 50: 6633-41. PMID 21710975 DOI: 10.1021/Bi2004476  0.321
2011 Collignon B, Schulz R, Smith JC, Baudry J. Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers. Journal of Computational Chemistry. 32: 1202-9. PMID 21387347 DOI: 10.1002/Jcc.21696  0.509
2011 Philip V, Harris J, Adams R, Nguyen D, Spiers J, Baudry J, Howell EE, Hinde RJ. A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-π pairs. Biochemistry. 50: 2939-50. PMID 21366334 DOI: 10.1021/Bi200066K  0.575
2011 Harris JB, Jenkins DD, Reyles J, Rickett S, Utley JM, Howell EE, Baudry J, Hinde RJ. Determining anion-quadrupole interactions among protein, DNA, and ligand molecules Bmc Bioinformatics. 12. DOI: 10.1186/1471-2105-12-S7-A5  0.603
2011 Reyles J, Miao Y, Baudry J, Smith JC. Dynamics Investigation of the Cytochrome P450cam Active Site Mutant Thr252ALA Biophysical Journal. 100: 222a. DOI: 10.1016/J.Bpj.2010.12.1423  0.492
2009 Spies MA, Reese JG, Dodd D, Pankow KL, Blanke SR, Baudry J. Determinants of catalytic power and ligand binding in glutamate racemase. Journal of the American Chemical Society. 131: 5274-84. PMID 19309142 DOI: 10.1021/Ja809660G  0.313
2008 Bondar AN, Baudry J, Suhai S, Fischer S, Smith JC. Key role of active-site water molecules in bacteriorhodopsin proton-transfer reactions. The Journal of Physical Chemistry. B. 112: 14729-41. PMID 18973373 DOI: 10.1021/Jp801916F  0.472
2007 Baudry J, Smith JC. Can proteins and crystals self-catalyze methyl rotations? The Journal of Physical Chemistry. B. 109: 20572-8. PMID 16853663 DOI: 10.1021/Jp053111Z  0.479
2006 Baudry J. van der Waals Interactions and Decrease of the Rotational Barrier of Methyl-Sized Rotators: A Theoretical Study Journal of the American Chemical Society. 128: 11088-11093. PMID 16925426 DOI: 10.1021/Ja060731K  0.326
2005 Wen Z, Baudry J, Berenbaum MR, Schuler MA. Ile115Leu mutation in the SRS1 region of an insect cytochrome P450 (CYP6B1) compromises substrate turnover via changes in a predicted product release channel. Protein Engineering, Design & Selection : Peds. 18: 191-9. PMID 15837716 DOI: 10.1093/Protein/Gzi023  0.308
2005 Ke N, Baudry J, Makris TM, Schuler MA, Sligar SG. A retinoic acid binding cytochrome P450: CYP120A1 from Synechocystis sp. PCC 6803. Archives of Biochemistry and Biophysics. 436: 110-20. PMID 15752715 DOI: 10.1016/J.Abb.2005.01.011  0.311
2005 Baudry J, Tajkhorshid E, Schulten K. Complementarities and convergence of results in bacteriorhodopsin trimer simulations. Biophysical Journal. 87: 1394-5; author reply. PMID 15298942 DOI: 10.1529/biophysj.104.041418  0.341
2005 Baudry J, Hergenrother PJ. Structure-based design and in silico virtual screening of combinatorial libraries: A combined chemical-computational project Journal of Chemical Education. 82: 890-894. DOI: 10.1021/Ed082P890  0.347
2004 Autenrieth F, Tajkhorshid E, Baudry J, Luthey-Schulten Z. Classical force field parameters for the heme prosthetic group of cytochrome c Journal of Computational Chemistry. 25: 1613-1622. PMID 15264255 DOI: 10.1002/Jcc.20079  0.344
2004 Li X, Baudry J, Berenbaum MR, Schuler MA. Structural and functional divergence of insect CYP6B proteins: From specialist to generalist cytochrome P450. Proceedings of the National Academy of Sciences of the United States of America. 101: 2939-44. PMID 14981232 DOI: 10.1073/Pnas.0308691101  0.351
2003 Rupasinghe S, Baudry J, Schuler MA. Common active site architecture and binding strategy of four phenylpropanoid P450s from Arabidopsis thaliana as revealed by molecular modeling. Protein Engineering. 16: 721-31. PMID 14600201 DOI: 10.1093/Protein/Gzg094  0.315
2003 Baudry J, Li W, Pan L, Berenbaum MR, Schuler MA. Molecular docking of substrates and inhibitors in the catalytic site of CYP6B1, an insect cytochrome p450 monooxygenase. Protein Engineering. 16: 577-87. PMID 12968075 DOI: 10.1093/Protein/Gzg075  0.355
2003 Sun J, Baudry J, Katzenellenbogen JA, Katzenellenbogen BS. Molecular basis for the subtype discrimination of the estrogen receptor-β-selective ligand, diarylpropionitrile Molecular Endocrinology. 17: 247-258. PMID 12554752 DOI: 10.1210/Me.2002-0341  0.334
2001 Isralewitz B, Baudry J, Gullingsrud J, Kosztin D, Schulten K. Steered molecular dynamics investigations of protein function. Journal of Molecular Graphics & Modelling. 19: 13-25. PMID 11381523 DOI: 10.1016/S1093-3263(00)00133-9  0.756
2001 Baudry J, Tajkhorshid E, Molnar F, Phillips J, Schulten K. Molecular Dynamics Study of Bacteriorhodopsin and the Purple Membrane The Journal of Physical Chemistry B. 105: 905-918. DOI: 10.1021/Jp000898E  0.498
2000 Tajkhorshid E, Baudry J, Schulten K, Suhai S. Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin. Biophysical Journal. 78: 683-93. PMID 10653781 DOI: 10.1016/S0006-3495(00)76626-4  0.489
1999 Baudry J, Crouzy S, Roux B, Smith JC. Simulation analysis of the retinal conformational equilibrium in dark-adapted bacteriorhodopsin. Biophysical Journal. 76: 1909-17. PMID 10096888 DOI: 10.1016/S0006-3495(99)77349-2  0.586
1999 Crouzy S, Baudry J, Smith JC, Roux B. Efficient calculation of two-dimensional adiabatic and free energy maps: Application to the isomerization of the C13?C14 and C15?N16 bonds in the retinal of bacteriorhodopsin Journal of Computational Chemistry. 20: 1644-1658. DOI: 10.1002/(Sici)1096-987X(19991130)20:15<1644::Aid-Jcc5>3.0.Co;2-Y  0.519
1997 Baudry J, Crouzy S, Roux B, Smith JC. Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics Journal of Chemical Information and Computer Sciences. 37: 1018-1024. DOI: 10.1021/Ci9702398  0.564
1994 Baudry J, Smith JC. Molecular mechanics analysis of peptide group hydrogen bonding cooperativity and influence on Φand Ψ rotational barriers Journal of Molecular Structure-Theochem. 308: 103-113. DOI: 10.1016/0166-1280(94)80096-0  0.452
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