Jeremy C. Smith - Publications

Molecular Biophysics Oak Ridge National Laboratory, Oak Ridge, TN, United States 

220 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
2020 Smith MD, Smith JC. Effects of sodium and calcium chloride ionic stresses on model yeast membranes revealed by molecular dynamics simulation. Chemistry and Physics of Lipids. 104980. PMID 33038307 DOI: 10.1016/j.chemphyslip.2020.104980  1
2020 Devarajan D, Liang L, Gu B, Brooks SC, Parks JM, Smith JC. Molecular Dynamics Simulation of the Structures, Dynamics, and Aggregation of Dissolved Organic Matter. Environmental Science & Technology. PMID 32985864 DOI: 10.1021/acs.est.0c01176  0.56
2020 Ishida T, Parks JM, Smith JC. Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion based on a Neutron Structure. Journal of the American Chemical Society. PMID 32959658 DOI: 10.1021/jacs.0c02148  0.56
2020 Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, Golosov AA, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, ... ... Smith JC, et al. Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. Biorxiv : the Preprint Server For Biology. PMID 32935106 DOI: 10.1101/2020.09.07.286344  1
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  1
2020 Gupta M, Ha K, Agarwal R, Quarles LD, Smith JC. Molecular Dynamics Analysis of The Binding of Human Interleukin-6 with Interleukin-6 α-Receptor. Proteins. PMID 32881084 DOI: 10.1002/prot.26002  1
2020 Aranha MP, Jewel YSM, Beckman RA, Weiner LM, Mitchell JC, Parks JM, Smith JC. Combining Three-Dimensional Modeling with Artificial Intelligence to Increase Specificity and Precision in Peptide-MHC Binding Predictions. Journal of Immunology (Baltimore, Md. : 1950). PMID 32878910 DOI: 10.4049/jimmunol.1900918  0.56
2020 Pingali SV, Smith MD, Liu SH, Rawal TB, Pu Y, Shah R, Evans BR, Urban VS, Davison BH, Cai CM, Ragauskas AJ, O'Neill HM, Smith JC, Petridis L. Deconstruction of biomass enabled by local demixing of cosolvents at cellulose and lignin surfaces. Proceedings of the National Academy of Sciences of the United States of America. PMID 32636260 DOI: 10.1073/pnas.1922883117  1
2020 Agarwal R, Shrestha UR, Chu XQ, Petridis L, Smith JC. Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study. Biophysical Journal. PMID 32533942 DOI: 10.1016/j.bpj.2020.05.021  1
2020 Parks JM, Smith JC. How to Discover Antiviral Drugs Quickly. The New England Journal of Medicine. PMID 32433861 DOI: 10.1056/NEJMcibr2007042  0.56
2020 Mostofian B, Johnson QR, Smith JC, Cheng X. Carotenoids promote lateral packing and condensation of lipid membranes. Physical Chemistry Chemical Physics : Pccp. PMID 32432296 DOI: 10.1039/d0cp01031f  1
2020 Agarwal R, Smith MD, Smith JC. Capturing Deuteration Effects in a Molecular Mechanics Force Field: Deuterated THF and the THF-Water Miscibility Gap. Journal of Chemical Theory and Computation. PMID 32175738 DOI: 10.1021/acs.jctc.9b01138  1
2020 Green AT, Moniruzzaman M, Cooper CJ, Walker JK, Smith JC, Parks JM, Zgurskaya HI. Discovery of multidrug efflux pump inhibitors with a novel chemical scaffold. Biochimica Et Biophysica Acta. General Subjects. 129546. PMID 32032658 DOI: 10.1016/j.bbagen.2020.129546  0.56
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  1
2019 Hwang H, Hazel A, Lian P, Smith JC, Gumbart JC, Parks JM. A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. Journal of Computational Chemistry. PMID 31721253 DOI: 10.1002/jcc.26098  0.56
2019 Lian P, Guo L, Devarajan D, Parks JM, Painter SL, Brooks SC, Smith JC. The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation. Journal of Computational Chemistry. PMID 31603259 DOI: 10.1002/jcc.26081  0.56
2019 Shrestha UR, Juneja P, Zhang Q, Gurumoorthy V, Borreguero JM, Urban V, Cheng X, Pingali SV, Smith JC, O'Neill HM, Petridis L. Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31548393 DOI: 10.1073/pnas.1907251116  1
2019 Close DM, Cooper CJ, Wang X, Chirania P, Gupta M, Ossyra JR, Giannone RJ, Engle N, Tschaplinski TJ, Smith JC, Hedstrom L, Parks JM, Michener JK. Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. Molecular Microbiology. PMID 31532038 DOI: 10.1111/mmi.14393  0.56
2019 Hazel A, Abdali N, Leus I, Parks JM, Smith JC, Zgurskaya HI, Gumbart JC. Conformational dynamics of AcrA govern multidrug efflux pump assembly. Acs Infectious Diseases. PMID 31517484 DOI: 10.1021/acsinfecdis.9b00273  0.56
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  1
2019 Demerdash O, Shrestha UR, Petridis L, Smith JC, Mitchell JC, Ramanathan A. Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins. Frontiers in Molecular Biosciences. 6: 64. PMID 31475155 DOI: 10.3389/fmolb.2019.00064  1
2019 Patri AS, Mostofian B, Pu Y, Ciaffone N, Soliman M, Smith MD, Kumar R, Cheng X, Wyman CE, Tetard L, Ragauskas AJ, Smith JC, Petridis L, Cai CM. A multifunctional co-solvent pair reveals molecular principles of biomass deconstruction. Journal of the American Chemical Society. PMID 31304747 DOI: 10.1021/jacs.8b10242  1
2019 Cheng X, Smith JC. Biological Membrane Organization and Cellular Signaling. Chemical Reviews. PMID 30747526 DOI: 10.1021/acs.chemrev.8b00439  1
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  1
2019 Darzynkiewicz ZM, Green AT, Abdali N, Hazel A, Fulton RL, Kimball J, Gryczynski Z, Gumbart JC, Parks JM, Smith JC, Zgurskaya HI. Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA. Biophysical Journal. PMID 30691677 DOI: 10.1016/j.bpj.2019.01.010  0.56
2019 Asaduzzaman A, Riccardi D, Afaneh AT, Cooper SJ, Smith JC, Wang F, Parks JM, Schreckenbach G. Environmental Mercury Chemistry - In Silico. Accounts of Chemical Research. PMID 30689347 DOI: 10.1021/acs.accounts.8b00454  1
2018 Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, ... ... Smith JC, et al. Neutron scattering in the biological sciences: progress and prospects. Acta Crystallographica. Section D, Structural Biology. 74: 1129-1168. PMID 30605130 DOI: 10.1107/S2059798318017503  1
2018 Krachtus D, Smith JC, Imhof P. Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase. Molecules (Basel, Switzerland). 23. PMID 30563005 DOI: 10.3390/molecules23123342  0.44
2018 Vural D, Smith JC, Petridis L. Dynamics of the lignin glass transition. Physical Chemistry Chemical Physics : Pccp. 20: 20504-20512. PMID 30046795 DOI: 10.1039/c8cp03144d  1
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  1
2018 Lian P, Johnston RC, Parks JM, Smith JC. Quantum Chemical Calculation of p Ks of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines and Thiols in Aqueous Solution. The Journal of Physical Chemistry. A. PMID 29633840 DOI: 10.1021/acs.jpca.8b01751  0.56
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  1
2018 Smith JC, Tan P, Petridis L, Hong L. Dynamic Neutron Scattering by Biological Systems. Annual Review of Biophysics. PMID 29561628 DOI: 10.1146/annurev-biophys-070317-033358  1
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  1
2018 Johnson QR, Mostofian B, Fuente Gomez G, Smith JC, Cheng X. Effects of carotenoids on lipid bilayers. Physical Chemistry Chemical Physics : Pccp. PMID 29349456 DOI: 10.1039/c7cp07126d  1
2018 Moyer P, Smith MD, Abdoulmoumine N, Chmely SC, Smith JC, Petridis L, Labbé N. Relationship between lignocellulosic biomass dissolution and physicochemical properties of ionic liquids composed of 3-methylimidazolium cations and carboxylate anions. Physical Chemistry Chemical Physics : Pccp. PMID 29313537 DOI: 10.1039/c7cp07195g  1
2017 Liu Z, Huang J, Tyagi M, O'Neill H, Zhang Q, Mamontov E, Jain N, Wang Y, Zhang J, Smith JC, Hong L. Dynamical Transition of Collective Motions in Dry Proteins. Physical Review Letters. 119: 048101. PMID 29341744 DOI: 10.1103/PhysRevLett.119.048101  0.56
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  1
2017 Smith MD, Cheng X, Petridis L, Mostofian B, Smith JC. Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis. Scientific Reports. 7: 14494. PMID 29101352 DOI: 10.1038/s41598-017-15048-7  1
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  1
2017 O'Neill H, Pingali SV, Petridis L, He J, Mamontov E, Hong L, Urban V, Evans B, Langan P, Smith JC, Davison BH. Dynamics of water bound to crystalline cellulose. Scientific Reports. 7: 11840. PMID 28928470 DOI: 10.1038/s41598-017-12035-w  1
2017 Polimeni M, Petridis L, Smith JC, Arcangeli C. Dynamics at a Peptide-TiO2 Anatase (101) Interface. The Journal of Physical Chemistry. B. PMID 28851213 DOI: 10.1021/acs.jpcb.7b04707  1
2017 Zhou J, Smith MD, Cooper SJ, Cheng X, Smith JC, Parks JM. Modeling of the Passive Permeation of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane. Environmental Science & Technology. PMID 28806072 DOI: 10.1021/acs.est.7b02204  1
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  0.56
2017 Cortini R, Cheng X, Smith JC. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 29: 084002. PMID 28092632 DOI: 10.1088/1361-648X/aa4e68  1
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  0.48
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  1
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  0.56
2016 Hong L, Jain N, Cheng X, Bernal A, Tyagi M, Smith JC. Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering. Science Advances. 2: e1600886. PMID 27757419 DOI: 10.1126/sciadv.1600886  1
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  1
2016 Mostofian B, Cai CM, Smith MD, Petridis L, Cheng X, Wyman CE, Smith JC. Local Phase Separation of Co-Solvents Enhances Pretreatment of Biomass for Bioenergy Applications. Journal of the American Chemical Society. PMID 27482599 DOI: 10.1021/jacs.6b03285  1
2016 Sangha AK, Petridis L, Cheng X, Smith JC. Relative Binding Affinities of Monolignols to Horseradish Peroxidase. The Journal of Physical Chemistry. B. PMID 27447548 DOI: 10.1021/acs.jpcb.6b00789  1
2016 Johnston RC, Zhou J, Smith JC, Parks JM. Toward quantitatively accurate calculation of the redox-associated acid-base and ligand binding equilibria of aquacobalamin. The Journal of Physical Chemistry. B. PMID 27391132 DOI: 10.1021/acs.jpcb.6b02701  1
2016 Lopez HD, Simakov NA, Smith JC, Lopez-Garriga J, Wymore T. Homolytic Cleavage of Both Heme-bound Hydrogen Peroxide and Hydrogen Sulfide Leads to the Formation of Sulfheme. The Journal of Physical Chemistry. B. PMID 27357070 DOI: 10.1021/acs.jpcb.6b02839  1
2016 Vural D, Hu X, Lindner B, Jain N, Miao Y, Cheng X, Liu Z, Hong L, Smith JC. Quasielastic neutron scattering in biology: Theory and applications. Biochimica Et Biophysica Acta. PMID 27316321 DOI: 10.1016/j.bbagen.2016.06.015  1
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  1
2016 Gerlits O, Wymore T, Das A, Shen CH, Parks JM, Smith JC, Weiss KL, Keen DA, Blakeley MP, Louis JM, Langan P, Weber IT, Kovalevsky A. Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site. Angewandte Chemie (International Ed. in English). PMID 26958828 DOI: 10.1002/anie.201509989  1
2016 Smith MD, Petridis L, Cheng X, Mostofian B, Smith JC. Enhanced sampling simulation analysis of the structure of lignin in the THF-water miscibility gap. Physical Chemistry Chemical Physics : Pccp. PMID 26862597 DOI: 10.1039/c5cp07088k  1
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  1
2016 Petridis L, Smith JC. Conformations of Low-Molecular-Weight Lignin Polymers in Water. Chemsuschem. PMID 26763657 DOI: 10.1002/cssc.201501350  0.76
2016 Smith MD, Mostofian B, Petridis L, Cheng X, Smith JC. Molecular Driving Forces Behind the Tetrahydrofuran-Water Miscibility Gap. The Journal of Physical Chemistry. B. PMID 26734991 DOI: 10.1021/acs.jpcb.5b09770  1
2016 Aggarwal M, Kovalevsky AY, Velazquez H, Fisher SZ, Smith JC, McKenna R. Neutron structure of human carbonic anhydrase II in complex with methazolamide: Mapping the solvent and hydrogen-bonding patterns of an effective clinical drug Iucrj. 3: 319-325. DOI: 10.1107/S2052252516010514  1
2016 Smith MD, Mostofian B, Cheng X, Petridis L, Cai CM, Wyman CE, Smith JC. Cosolvent pretreatment in cellulosic biofuel production: Effect of tetrahydrofuran-water on lignin structure and dynamics Green Chemistry. 18: 1268-1277. DOI: 10.1039/c5gc01952d  1
2015 Vermaas JV, Petridis L, Qi X, Schulz R, Lindner B, Smith JC. Mechanism of lignin inhibition of enzymatic biomass deconstruction. Biotechnology For Biofuels. 8: 217. PMID 26697106 DOI: 10.1186/s13068-015-0379-8  1
2015 Gopal Vandavasi V, Putnam DK, Zhang Q, Petridis L, Heller WT, Nixon BT, Haigler CH, Kalluri U, Coates L, Langan P, Smith JC, Meiler J, O'Neill H. A Structural Study of CESA1 catalytic domain of Arabidopsis thaliana Cellulose Synthesis Complex: Evidence for CESA trimers. Plant Physiology. PMID 26556795 DOI: 10.1104/pp.15.01356  0.76
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  1
2015 Nickels JD, Cheng X, Mostofian B, Stanley C, Lindner B, Heberle FA, Perticaroli S, Feygenson M, Egami T, Standaert RF, Smith JC, Myles DA, Ohl M, Katsaras J. Mechanical properties of nanoscopic lipid domains. Journal of the American Chemical Society. PMID 26415030 DOI: 10.1021/jacs.5b08894  1
2015 Nickels JD, Smith JC, Cheng X. Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes. Chemistry and Physics of Lipids. PMID 26232661 DOI: 10.1016/j.chemphyslip.2015.07.012  1
2015 Yang X, Cushman JC, Borland AM, Edwards EJ, Wullschleger SD, Tuskan GA, Owen NA, Griffiths H, Smith JA, De Paoli HC, Weston DJ, Cottingham R, Hartwell J, Davis SC, Silvera K, et al. A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world. The New Phytologist. 207: 491-504. PMID 26153373 DOI: 10.1111/nph.13393  0.44
2015 Vural D, Hong L, Smith JC, Glyde HR. Motional displacements in proteins: The origin of wave-vector-dependent values. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 91: 052705. PMID 26066197 DOI: 10.1103/PhysRevE.91.052705  1
2015 Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, Del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, ... ... Smith JC, et al. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. The Journal of Membrane Biology. 248: 611-40. PMID 26063070 DOI: 10.1007/s00232-015-9802-0  1
2015 Riccardi D, Parks JM, Johs A, Smith JC. HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales. Journal of Chemical Information and Modeling. 55: 721-6. PMID 25793330 DOI: 10.1021/ci500359e  1
2015 Daidone I, Thukral L, Smith JC, Amadei A. Monitoring the folding kinetics of a β-hairpin by time-resolved IR spectroscopy in silico. The Journal of Physical Chemistry. B. 119: 4849-56. PMID 25777154 DOI: 10.1021/acs.jpcb.5b01477  1
2015 Carmona C, Langan P, Smith JC, Petridis L. Why genetic modification of lignin leads to low-recalcitrance biomass. Physical Chemistry Chemical Physics : Pccp. 17: 358-64. PMID 25384960 DOI: 10.1039/c4cp05004e  0.76
2015 Lindner B, Petridis L, Langan P, Smith JC. Determination of cellulose crystallinity from powder diffraction diagrams. Biopolymers. 103: 67-73. PMID 25269646 DOI: 10.1002/bip.22555  1
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  1
2015 Wolter T, Elstner M, Fischer S, Smith JC, Bondar AN. Mechanism by which untwisting of retinal leads to productive bacteriorhodopsin photocycle states. The Journal of Physical Chemistry. B. 119: 2229-40. PMID 25196390 DOI: 10.1021/jp505818r  1
2015 Hu X, Hong L, Dean Smith M, Neusius T, Cheng X, Smith JC. The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time Nature Physics. DOI: 10.1038/nphys3553  0.56
2015 Abraham MJ, Murtola T, Schulz R, Páall S, Smith JC, Hess B, Lindah E. Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Softwarex. 1: 19-25. DOI: 10.1016/j.softx.2015.06.001  1
2015 Nickels JD, Smith JC, Cheng X. Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes Chemistry and Physics of Lipids. DOI: 10.1016/j.chemphyslip.2015.07.012  1
2014 Erler J, Zhang R, Petridis L, Cheng X, Smith JC, Langowski J. The role of histone tails in the nucleosome: a computational study. Biophysical Journal. 107: 2911-22. PMID 25517156 DOI: 10.1016/j.bpj.2014.10.065  1
2014 Lian P, Guo HB, Riccardi D, Dong A, Parks JM, Xu Q, Pai EF, Miller SM, Wei DQ, Smith JC, Guo H. X-ray structure of a Hg2+ complex of mercuric reductase (MerA) and quantum mechanical/molecular mechanical study of Hg2+ transfer between the C-terminal and buried catalytic site cysteine pairs. Biochemistry. 53: 7211-22. PMID 25343681 DOI: 10.1021/bi500608u  1
2014 Petridis L, O'Neill HM, Johnsen M, Fan B, Schulz R, Mamontov E, Maranas J, Langan P, Smith JC. Hydration control of the mechanical and dynamical properties of cellulose. Biomacromolecules. 15: 4152-9. PMID 25325376 DOI: 10.1021/bm5011849  1
2014 Mostofian B, Cheng X, Smith JC. Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride. The Journal of Physical Chemistry. B. 118: 11037-49. PMID 25180945 DOI: 10.1021/jp502889c  1
2014 Langan P, Sangha AK, Wymore T, Parks JM, Yang ZK, Hanson BL, Fisher Z, Mason SA, Blakeley MP, Forsyth VT, Glusker JP, Carrell HL, Smith JC, Keen DA, Graham DE, et al. L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study. Structure (London, England : 1993). 22: 1287-300. PMID 25132082 DOI: 10.1016/j.str.2014.07.002  1
2014 Hong L, Sharp MA, Poblete S, Biehl R, Zamponi M, Szekely N, Appavou MS, Winkler RG, Nauss RE, Johs A, Parks JM, Yi Z, Cheng X, Liang L, Ohl M, ... ... Smith JC, et al. Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase. Biophysical Journal. 107: 393-400. PMID 25028881 DOI: 10.1016/j.bpj.2014.06.013  1
2014 Moritsugu K, Kidera A, Smith JC. Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes. The Journal of Physical Chemistry. B. 118: 8559-65. PMID 24999844 DOI: 10.1021/jp503956m  1
2014 T RR, Smith JC, Krishnan M. Hidden regularity and universal classification of fast side chain motions in proteins. Journal of the American Chemical Society. 136: 8590-605. PMID 24844417 DOI: 10.1021/ja5024783  1
2014 Hong L, Smolin N, Smith JC. de Gennes narrowing describes the relative motion of protein domains. Physical Review Letters. 112: 158102. PMID 24785076 DOI: 10.1103/PhysRevLett.112.158102  1
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  1
2014 Wymore T, Field MJ, Langan P, Smith JC, Parks JM. Hydrolysis of DFP and the nerve agent (S)-sarin by DFPase proceeds along two different reaction pathways: implications for engineering bioscavengers. The Journal of Physical Chemistry. B. 118: 4479-89. PMID 24720808 DOI: 10.1021/jp410422c  0.76
2014 Srinivas G, Cheng X, Smith JC. Coarse-grain model for natural cellulose fibrils in explicit water. The Journal of Physical Chemistry. B. 118: 3026-34. PMID 24564237 DOI: 10.1021/jp407953p  1
2014 Zhou J, Riccardi D, Beste A, Smith JC, Parks JM. Mercury methylation by HgcA: theory supports carbanion transfer to Hg(II). Inorganic Chemistry. 53: 772-7. PMID 24377658 DOI: 10.1021/ic401992y  0.76
2014 Sangha AK, Davison BH, Standaert RF, Davis MF, Smith JC, Parks JM. Chemical factors that control lignin polymerization. The Journal of Physical Chemistry. B. 118: 164-70. PMID 24341896 DOI: 10.1021/jp411998t  0.76
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  1
2014 Mostofian B, Smith JC, Cheng X. Simulation of a cellulose fiber in ionic liquid suggests a synergistic approach to dissolution Cellulose. 21: 983-997. DOI: 10.1007/s10570-013-0018-0  1
2014 Lian P, Guo HB, Smith JC, Wei DQ, Guo H. Catalytic mechanism and origin of high activity of cellulase TmCel12A at high temperature: A quantum mechanical/molecular mechanical study Cellulose. 21: 937-949. DOI: 10.1007/s10570-013-0011-7  1
2014 Hong L, Petridis L, Smith JC. Biomolecular structure and dynamics with neutrons: The view from simulation Israel Journal of Chemistry. DOI: 10.1002/ijch.201300137  1
2013 Riccardi D, Guo HB, Parks JM, Gu B, Liang L, Smith JC. Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations. Journal of Chemical Theory and Computation. 9: 555-69. PMID 26589054 DOI: 10.1021/ct300296k  1
2013 Vural D, Hong L, Smith JC, Glyde HR. Long-time mean-square displacements in proteins. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 88: 052706. PMID 24329295 DOI: 10.1103/PhysRevE.88.052706  0.76
2013 Smith JC, Roux B. Eppur si muove! The 2013 Nobel Prize in Chemistry. Structure (London, England : 1993). 21: 2102-5. PMID 24315458 DOI: 10.1016/j.str.2013.11.005  1
2013 Yi Z, Lindner B, Prinz JH, Noé F, Smith JC. Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling. The Journal of Chemical Physics. 139: 175102. PMID 24206335 DOI: 10.1063/1.4824071  0.76
2013 Lindner B, Yi Z, Prinz JH, Smith JC, Noé F. Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models. The Journal of Chemical Physics. 139: 175101. PMID 24206334 DOI: 10.1063/1.4824070  0.76
2013 Chen Q, Buolamwini JK, Smith JC, Li A, Xu Q, Cheng X, Wei D. Impact of resistance mutations on inhibitor binding to HIV-1 integrase. Journal of Chemical Information and Modeling. 53: 3297-307. PMID 24205814 DOI: 10.1021/ci400537n  1
2013 Godec A, Smith JC, Merzel F. Soft collective fluctuations governing hydrophobic association. Physical Review Letters. 111: 127801. PMID 24093302  0.6
2013 Lindner B, Petridis L, Schulz R, Smith JC. Solvent-driven preferential association of lignin with regions of crystalline cellulose in molecular dynamics simulation. Biomacromolecules. 14: 3390-8. PMID 23980921 DOI: 10.1021/bm400442n  1
2013 Devarajan A, Markutsya S, Lamm MH, Cheng X, Smith JC, Baluyut JY, Kholod Y, Gordon MS, Windus TL. Ab initio study of molecular interactions in cellulose Iα. The Journal of Physical Chemistry. B. 117: 10430-43. PMID 23937275 DOI: 10.1021/jp406266u  1
2013 Miao Y, Hong L, Yi Z, Smith JC. Zaccai neutron resilience and site-specific hydration dynamics in a globular protein. The European Physical Journal. E, Soft Matter. 36: 72. PMID 23852576 DOI: 10.1140/epje/i2013-13072-5  0.76
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  1
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  1
2013 Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, Lindahl E. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England). 29: 845-54. PMID 23407358 DOI: 10.1093/bioinformatics/btt055  1
2013 Parks JM, Johs A, Podar M, Bridou R, Hurt RA, Smith SD, Tomanicek SJ, Qian Y, Brown SD, Brandt CC, Palumbo AV, Smith JC, Wall JD, Elias DA, Liang L. The genetic basis for bacterial mercury methylation. Science (New York, N.Y.). 339: 1332-5. PMID 23393089 DOI: 10.1126/science.1230667  1
2013 Hong L, Glass DC, Nickels JD, Perticaroli S, Yi Z, Tyagi M, O'Neill H, Zhang Q, Sokolov AP, Smith JC. Elastic and conformational softness of a globular protein. Physical Review Letters. 110: 028104. PMID 23383942 DOI: 10.1103/PhysRevLett.110.028104  1
2013 Riccardi D, Guo HB, Parks JM, Gu B, Summers AO, Miller SM, Liang L, Smith JC. Why mercury prefers soft ligands Journal of Physical Chemistry Letters. 4: 2317-2322. DOI: 10.1021/jz401075b  1
2013 Riccardi D, Guo HB, Parks JM, Gu B, Liang L, Smith JC. Cluster-continuum calculations of hydration free energies of anions and group 12 divalent cations Journal of Chemical Theory and Computation. 9: 555-569. DOI: 10.1021/ct300296k  1
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  1
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  1
2012 Guo HB, He F, Gu B, Liang L, Smith JC. Time-dependent density functional theory assessment of UV absorption of benzoic acid derivatives. The Journal of Physical Chemistry. A. 116: 11870-9. PMID 23134517 DOI: 10.1021/jp3084293  0.44
2012 Nickels JD, O'Neill H, Hong L, Tyagi M, Ehlers G, Weiss KL, Zhang Q, Yi Z, Mamontov E, Smith JC, Sokolov AP. Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP. Biophysical Journal. 103: 1566-75. PMID 23062349 DOI: 10.1016/j.bpj.2012.08.046  1
2012 Daidone I, Iacobucci C, McLain SE, Smith JC. Alteration of water structure by peptide clusters revealed by neutron scattering in the small-angle region (below 1 Å(-1)). Biophysical Journal. 103: 1518-24. PMID 23062344 DOI: 10.1016/j.bpj.2012.08.010  1
2012 Hong L, Cheng X, Glass DC, Smith JC. Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core. Physical Review Letters. 108: 238102. PMID 23003993 DOI: 10.1103/PhysRevLett.108.238102  1
2012 Tschaplinski TJ, Standaert RF, Engle NL, Martin MZ, Sangha AK, Parks JM, Smith JC, Samuel R, Jiang N, Pu Y, Ragauskas AJ, Hamilton CY, Fu C, Wang ZY, Davison BH, et al. Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog. Biotechnology For Biofuels. 5: 71. PMID 22998926 DOI: 10.1186/1754-6834-5-71  1
2012 Ulmschneider JP, Smith JC, Ulmschneider MB, Ulrich AS, Strandberg E. Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations. Biophysical Journal. 103: 472-82. PMID 22947863 DOI: 10.1016/j.bpj.2012.06.040  1
2012 Glass DC, Moritsugu K, Cheng X, Smith JC. REACH coarse-grained simulation of a cellulose fiber. Biomacromolecules. 13: 2634-44. PMID 22937726 DOI: 10.1021/bm300460f  1
2012 Bere?niak T, Jäschke A, Smith JC, Imhof P. Stereoselection in the Diels-Alderase ribozyme: a molecular dynamics study. Journal of Computational Chemistry. 33: 1603-14. PMID 22549366 DOI: 10.1002/jcc.22993  0.32
2012 Sangha AK, Parks JM, Standaert RF, Ziebell A, Davis M, Smith JC. Radical coupling reactions in lignin synthesis: a density functional theory study. The Journal of Physical Chemistry. B. 116: 4760-8. PMID 22475051 DOI: 10.1021/jp2122449  1
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  1
2012 Krishnan M, Smith JC. Reconstruction of protein side-chain conformational free energy surfaces from NMR-derived methyl axis order parameters. The Journal of Physical Chemistry. B. 116: 4124-33. PMID 22401582 DOI: 10.1021/jp2104853  0.56
2012 Voltz K, Trylska J, Calimet N, Smith JC, Langowski J. Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study. Biophysical Journal. 102: 849-58. PMID 22385856 DOI: 10.1016/j.bpj.2011.11.4028  1
2012 Pool R, Heringa J, Hoefling M, Schulz R, Smith JC, Feenstra KA. Enabling grand-canonical Monte Carlo: extending the flexibility of GROMACS through the GromPy python interface module. Journal of Computational Chemistry. 33: 1207-14. PMID 22370965 DOI: 10.1002/jcc.22947  1
2012 Ellingson SR, Dakshanamurthy S, Brown M, Smith JC, Baudry J. Accelerating virtual high-throughput ligand docking: Screening one million compounds using a petascale supercomputer Ecmls 2012 - 3rd International Emerging Computational Methods For the Life Sciences Workshop. 33-37. DOI: 10.1145/2483954.2483961  1
2011 Srinivas G, Cheng X, Smith JC. A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils. Journal of Chemical Theory and Computation. 7: 2539-48. PMID 26606627 DOI: 10.1021/ct200181t  0.76
2011 Godec A, Smith JC, Merzel F. Increase of both order and disorder in the first hydration shell with increasing solute polarity. Physical Review Letters. 107: 267801. PMID 22243182  0.6
2011 Biswas M, Voltz K, Smith JC, Langowski J. Role of histone tails in structural stability of the nucleosome. Plos Computational Biology. 7: e1002279. PMID 22207822 DOI: 10.1371/journal.pcbi.1002279  0.76
2011 Mostofian B, Smith JC, Cheng X. The solvation structures of cellulose microfibrils in ionic liquids. Interdisciplinary Sciences, Computational Life Sciences. 3: 308-20. PMID 22179764 DOI: 10.1007/s12539-011-0111-8  1
2011 Hong L, Smolin N, Lindner B, Sokolov AP, Smith JC. Three classes of motion in the dynamic neutron-scattering susceptibility of a globular protein. Physical Review Letters. 107: 148102. PMID 22107237  0.56
2011 Petridis L, Schulz R, Smith JC. Simulation analysis of the temperature dependence of lignin structure and dynamics. Journal of the American Chemical Society. 133: 20277-87. PMID 22035184 DOI: 10.1021/ja206839u  1
2011 Hu X, Elghobashi-Meinhardt N, Gembris D, Smith JC. Response of water to electric fields at temperatures below the glass transition: a molecular dynamics analysis. The Journal of Chemical Physics. 135: 134507. PMID 21992324 DOI: 10.1063/1.3643077  0.56
2011 Thukral L, Daidone I, Smith JC. Structured pathway across the transition state for peptide folding revealed by molecular dynamics simulations. Plos Computational Biology. 7: e1002137. PMID 21931542 DOI: 10.1371/journal.pcbi.1002137  1
2011 Klein HC, Cheng X, Smith JC, Shen T. Transfer matrix approach to the hydrogen-bonding in cellulose Iα fibrils describes the recalcitrance to thermal deconstruction. The Journal of Chemical Physics. 135: 085106. PMID 21895224 DOI: 10.1063/1.3626274  0.76
2011 Johs A, Harwood IM, Parks JM, Nauss RE, Smith JC, Liang L, Miller SM. Structural characterization of intramolecular Hg(2+) transfer between flexibly linked domains of mercuric ion reductase. Journal of Molecular Biology. 413: 639-56. PMID 21893070 DOI: 10.1016/j.jmb.2011.08.042  0.76
2011 Ulmschneider JP, Smith JC, White SH, Ulmschneider MB. In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions. Journal of the American Chemical Society. 133: 15487-95. PMID 21861483 DOI: 10.1021/ja204042f  0.76
2011 Zahran M, Berezniak T, Imhof P, Smith JC. Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease. Febs Letters. 585: 2739-43. PMID 21835176 DOI: 10.1016/j.febslet.2011.07.036  0.76
2011 Brown SD, Guss AM, Karpinets TV, Parks JM, Smolin N, Yang S, Land ML, Klingeman DM, Bhandiwad A, Rodriguez M, Raman B, Shao X, Mielenz JR, Smith JC, Keller M, et al. Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum. Proceedings of the National Academy of Sciences of the United States of America. 108: 13752-7. PMID 21825121 DOI: 10.1073/pnas.1102444108  0.76
2011 Petridis L, Pingali SV, Urban V, Heller WT, O'Neill HM, Foston M, Ragauskas A, Smith JC. Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 83: 061911. PMID 21797407 DOI: 10.1103/PhysRevE.83.061911  0.76
2011 Pingali SV, O'Neill HM, McGaughey J, Urban VS, Rempe CS, Petridis L, Smith JC, Evans BR, Heller WT. Small angle neutron scattering reveals pH-dependent conformational changes in Trichoderma reesei cellobiohydrolase I: implications for enzymatic activity. The Journal of Biological Chemistry. 286: 32801-9. PMID 21784865 DOI: 10.1074/jbc.M111.263004  0.76
2011 Prinz JH, Chodera JD, Pande VS, Swope WC, Smith JC, Noé F. Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. The Journal of Chemical Physics. 134: 244108. PMID 21721613 DOI: 10.1063/1.3592153  0.76
2011 Daidone I, Di Nola A, Smith JC. Molecular origin of Gerstmann-Sträussler-Scheinker syndrome: insight from computer simulation of an amyloidogenic prion peptide. Biophysical Journal. 100: 3000-7. PMID 21689534 DOI: 10.1016/j.bpj.2011.04.053  1
2011 Splettstoesser T, Holmes KC, Noé F, Smith JC. Structural modeling and molecular dynamics simulation of the actin filament. Proteins. 79: 2033-43. PMID 21557314 DOI: 10.1002/prot.23017  0.76
2011 Balog E, Perahia D, Smith JC, Merzel F. Vibrational softening of a protein on ligand binding. The Journal of Physical Chemistry. B. 115: 6811-7. PMID 21553905 DOI: 10.1021/jp108493g  0.6
2011 Neusius T, Daidone I, Sokolov IM, Smith JC. Configurational subdiffusion of peptides: a network study. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 83: 021902. PMID 21405858  1
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  1
2011 Noé F, Doose S, Daidone I, Löllmann M, Sauer M, Chodera JD, Smith JC. Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proceedings of the National Academy of Sciences of the United States of America. 108: 4822-7. PMID 21368203 DOI: 10.1073/pnas.1004646108  1
2011 Bondar AN, Fischer S, Smith JC. Water pathways in the bacteriorhodopsin proton pump. The Journal of Membrane Biology. 239: 73-84. PMID 21113780 DOI: 10.1007/s00232-010-9329-3  0.44
2011 Prinz JH, Held M, Smith JC, Noé F. Efficient computation, sensitivity, and error analysis of committor probabilities for complex dynamical processes Multiscale Modeling and Simulation. 9: 545-567. DOI: 10.1137/100789191  0.76
2011 Guo HB, Parks JM, Johs A, Smith JC. Mercury Detoxification by Bacteria: Simulations of Transcription Activation and Mercury-Carbon Bond Cleavage Modeling of Molecular Properties. 311-324. DOI: 10.1002/9783527636402.ch20  1
2010 Saharay M, Guo H, Smith JC. Catalytic mechanism of cellulose degradation by a cellobiohydrolase, CelS. Plos One. 5: e12947. PMID 20967294 DOI: 10.1371/journal.pone.0012947  0.44
2010 Lopez M, Kurkal-Siebert V, Dunn RV, Tehei M, Finney JL, Smith JC, Daniel RM. Activity and dynamics of an enzyme, pig liver esterase, in near-anhydrous conditions. Biophysical Journal. 99: L62-4. PMID 20959076 DOI: 10.1016/j.bpj.2010.07.066  0.48
2010 Bere?niak T, Zahran M, Imhof P, Jäschke A, Smith JC. Magnesium-dependent active-site conformational selection in the Diels-Alderase ribozyme. Journal of the American Chemical Society. 132: 12587-96. PMID 20722413 DOI: 10.1021/ja101370e  1
2010 Zahran M, Daidone I, Smith JC, Imhof P. Mechanism of DNA recognition by the restriction enzyme EcoRV. Journal of Molecular Biology. 401: 415-32. PMID 20600128 DOI: 10.1016/j.jmb.2010.06.026  0.76
2010 Yang S, Land ML, Klingeman DM, Pelletier DA, Lu TY, Martin SL, Guo HB, Smith JC, Brown SD. Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America. 107: 10395-400. PMID 20484677 DOI: 10.1073/pnas.0914506107  1
2010 Guo HB, Johs A, Parks JM, Olliff L, Miller SM, Summers AO, Liang L, Smith JC. Structure and conformational dynamics of the metalloregulator MerR upon binding of Hg(II). Journal of Molecular Biology. 398: 555-68. PMID 20303978 DOI: 10.1016/j.jmb.2010.03.020  1
2010 Ulmschneider MB, Doux JP, Killian JA, Smith JC, Ulmschneider JP. Mechanism and kinetics of peptide partitioning into membranes from all-atom simulations of thermostable peptides. Journal of the American Chemical Society. 132: 3452-60. PMID 20163187 DOI: 10.1021/ja909347x  1
2010 Daidone I, Neuweiler H, Doose S, Sauer M, Smith JC. Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains. Plos Computational Biology. 6: e1000645. PMID 20098498 DOI: 10.1371/journal.pcbi.1000645  1
2009 Schulz R, Lindner B, Petridis L, Smith JC. Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer. Journal of Chemical Theory and Computation. 5: 2798-808. PMID 26631792 DOI: 10.1021/ct900292r  1
2009 Ulmschneider JP, Doux JP, Killian JA, Smith JC, Ulmschneider MB. Peptide Partitioning and Folding into Lipid Bilayers. Journal of Chemical Theory and Computation. 5: 2202-5. PMID 26616605 DOI: 10.1021/ct900256k  0.76
2009 Thukral L, Smith JC, Daidone I. Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations. Journal of the American Chemical Society. 131: 18147-52. PMID 19919102 DOI: 10.1021/ja9064365  1
2009 Xu Q, Chu YZ, Guo HB, Smith JC, Guo H. Energy triplets for writing epigenetic marks: insights from QM/MM free-energy simulations of protein lysine methyltransferases. Chemistry (Weinheim An Der Bergstrasse, Germany). 15: 12596-9. PMID 19882600 DOI: 10.1002/chem.200902297  0.44
2009 Parks JM, Guo H, Momany C, Liang L, Miller SM, Summers AO, Smith JC. Mechanism of Hg-C protonolysis in the organomercurial lyase MerB. Journal of the American Chemical Society. 131: 13278-85. PMID 19719173 DOI: 10.1021/ja9016123  1
2009 Moritsugu K, Kurkal-Siebert V, Smith JC. REACH coarse-grained normal mode analysis of protein dimer interaction dynamics. Biophysical Journal. 97: 1158-67. PMID 19686664 DOI: 10.1016/j.bpj.2009.05.015  0.32
2009 Imhof P, Fischer S, Smith JC. Catalytic mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: a quantum mechanical/molecular mechanical analysis. Biochemistry. 48: 9061-75. PMID 19678693 DOI: 10.1021/bi900585m  0.44
2009 Neusius T, Sokolov IM, Smith JC. Subdiffusion in time-averaged, confined random walks. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 80: 011109. PMID 19658655  1
2009 Krishnan M, Smith JC. Response of small-scale, methyl rotors to protein-ligand association: a simulation analysis of calmodulin-peptide binding. Journal of the American Chemical Society. 131: 10083-91. PMID 19621963 DOI: 10.1021/ja901276n  0.56
2009 Xu J, Crowley MF, Smith JC. Building a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulation. Protein Science : a Publication of the Protein Society. 18: 949-59. PMID 19384997 DOI: 10.1002/pro.105  1
2009 Schulz R, Krishnan M, Daidone I, Smith JC. Instantaneous normal modes and the protein glass transition. Biophysical Journal. 96: 476-84. PMID 19167298 DOI: 10.1016/j.bpj.2008.10.007  1
2009 Splettstoesser T, Noé F, Oda T, Smith JC. Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state. Proteins. 76: 353-64. PMID 19156817 DOI: 10.1002/prot.22350  0.4
2009 Petridis L, Smith JC. A molecular mechanics force field for lignin. Journal of Computational Chemistry. 30: 457-67. PMID 18677707 DOI: 10.1002/jcc.21075  1
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  1
2008 McLain SE, Soper AK, Daidone I, Smith JC, Watts A. Charge-based interactions between peptides observed as the dominant force for association in aqueous solution. Angewandte Chemie (International Ed. in English). 47: 9059-62. PMID 18937237 DOI: 10.1002/anie.200802679  1
2008 Noé F, Daidone I, Smith JC, di Nola A, Amadei A. Solvent electrostriction-driven peptide folding revealed by quasi-Gaussian entropy theory and molecular dynamics simulation. The Journal of Physical Chemistry. B. 112: 11155-63. PMID 18698708 DOI: 10.1021/jp801391t  1
2008 Neusius T, Daidone I, Sokolov IM, Smith JC. Subdiffusion in peptides originates from the fractal-like structure of configuration space. Physical Review Letters. 100: 188103. PMID 18518418  1
2008 Kurkal-Siebert V, Agarwal R, Smith JC. Hydration-dependent dynamical transition in protein: protein interactions at approximately 240 K. Physical Review Letters. 100: 138102. PMID 18518001 DOI: 10.1103/PhysRevLett.100.138102  0.32
2008 Meinhold L, Clement D, Tehei M, Daniel R, Finney JL, Smith JC. Protein dynamics and stability: the distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scattering. Biophysical Journal. 94: 4812-8. PMID 18310248 DOI: 10.1529/biophysj.107.121418  0.48
2008 Voltz K, Trylska J, Tozzini V, Kurkal-Siebert V, Langowski J, Smith J. Coarse-grained force field for the nucleosome from self-consistent multiscaling. Journal of Computational Chemistry. 29: 1429-39. PMID 18270964 DOI: 10.1002/jcc.20902  0.76
2007 Daidone I, Ulmschneider MB, Di Nola A, Amadei A, Smith JC. Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding. Proceedings of the National Academy of Sciences of the United States of America. 104: 15230-5. PMID 17881585 DOI: 10.1073/pnas.0701401104  1
2007 de Hatten X, Cournia Z, Huc I, Smith JC, Metzler-Nolte N. Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics. Chemistry (Weinheim An Der Bergstrasse, Germany). 13: 8139-52. PMID 17763506 DOI: 10.1002/chem.200700358  1
2007 Noé F, Horenko I, Schütte C, Smith JC. Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states. The Journal of Chemical Physics. 126: 155102. PMID 17461666 DOI: 10.1063/1.2714539  0.76
2006 Imhof P, Noé F, Fischer S, Smith JC. AM1/d Parameters for Magnesium in Metalloenzymes. Journal of Chemical Theory and Computation. 2: 1050-6. PMID 26633065 DOI: 10.1021/ct600092c  0.76
2006 Noé F, Krachtus D, Smith JC, Fischer S. Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins. Journal of Chemical Theory and Computation. 2: 840-57. PMID 26626691 DOI: 10.1021/ct050162r  0.76
2006 Balog E, Smith JC, Perahia D. Conformational heterogeneity and low-frequency vibrational modes of proteins. Physical Chemistry Chemical Physics : Pccp. 8: 5543-8. PMID 17136269 DOI: 10.1039/b610075a  0.6
2006 Smith JC. Tight in Titin Structure. 14: 389-390. PMID 16531221 DOI: 10.1016/j.str.2006.02.001  1
2006 Tehei M, Smith JC, Monk C, Ollivier J, Oettl M, Kurkal V, Finney JL, Daniel RM. Dynamics of immobilized and native Escherichia coli dihydrofolate reductase by quasielastic neutron scattering. Biophysical Journal. 90: 1090-7. PMID 16258053 DOI: 10.1529/biophysj.105.062182  0.48
2006 Kurkal-Siebert V, Daniel RM, Finney JL, Tehei M, Dunn RV, Smith JC. Enzyme hydration, activity and flexibility: A neutron scattering approach Journal of Non-Crystalline Solids. 352: 4387-4393. DOI: 10.1016/j.jnoncrysol.2006.01.115  0.48
2005 Tournier AL, Réat V, Dunn R, Daniel R, Smith JC, Finney J. Temperature and timescale dependence of protein dynamics in methanol : water mixtures. Physical Chemistry Chemical Physics : Pccp. 7: 1388-93. PMID 19787959 DOI: 10.1039/b416103c  0.4
2005 Jagoda M, Warzeska S, Pritzkow H, Wadepohl H, Imhof P, Smith JC, Krämer R. Catalytic transesterification of dialkyl phosphates by a bioinspired dicopper(II) macrocyclic complex. Journal of the American Chemical Society. 127: 15061-70. PMID 16248645 DOI: 10.1021/ja051357b  0.32
2005 Kurkal V, Daniel RM, Finney JL, Tehei M, Dunn RV, Smith JC. Enzyme activity and flexibility at very low hydration. Biophysical Journal. 89: 1282-7. PMID 15894640 DOI: 10.1529/biophysj.104.058677  0.48
2005 Fischer S, Windshügel B, Horak D, Holmes KC, Smith JC. Structural mechanism of the recovery stroke in the myosin molecular motor. Proceedings of the National Academy of Sciences of the United States of America. 102: 6873-8. PMID 15863618 DOI: 10.1073/pnas.0408784102  1
2005 Noé F, Ille F, Smith JC, Fischer S. Automated computation of low-energy pathways for complex rearrangements in proteins: application to the conformational switch of Ras p21. Proteins. 59: 534-44. PMID 15778967 DOI: 10.1002/prot.20422  0.76
2004 Efferth T, Bachli EB, Schwarzl SM, Goede JS, West C, Smith JC, Beutler E. Glucose-6-phosphate dehydrogenase (G6PD) deficiency-type Zurich: a splice site mutation as an uncommon mechanism producing enzyme deficiency. Blood. 104: 2608. PMID 15466166 DOI: 10.1182/blood-2004-06-2135  0.32
2004 Becker T, Hayward JA, Finney JL, Daniel RM, Smith JC. Neutron frequency windows and the protein dynamical transition. Biophysical Journal. 87: 1436-44. PMID 15345526 DOI: 10.1529/biophysj.104.042226  0.48
2004 Smith JC, Merzel F, Bondar AN, Tournier A, Fischer S, Kornyshev A, Daniel RM, Halle B, Wilson K. Structure, dynamics and reactions of protein hydration water Philosophical Transactions of the Royal Society B: Biological Sciences. 359: 1181-1190. PMID 15306375 DOI: 10.1098/rstb.2004.1497  1
2003 Noé F, Schwarzl SM, Fischer S, Smith JC. Computational tools for analysing structural changes in proteins in solution. Applied Bioinformatics. 2: S11-7. PMID 15130811  0.76
2003 Hayward JA, Finney JL, Daniel RM, Smith JC. Molecular dynamics decomposition of temperature-dependent elastic neutron scattering by a protein solution. Biophysical Journal. 85: 679-85. PMID 12885619 DOI: 10.1016/S0006-3495(03)74511-1  0.48
2003 Daniel RM, Finney JL, Smith JC. The dynamic transition in proteins may have a simple explanation. Faraday Discussions. 122: 163-9; discussion 17. PMID 12555856  0.48
2003 Daniel RM, Dunn RV, Finney JL, Smith JC. The role of dynamics in enzyme activity. Annual Review of Biophysics and Biomolecular Structure. 32: 69-92. PMID 12471064 DOI: 10.1146/annurev.biophys.32.110601.142445  0.48
2000 Réat V, Dunn R, Ferrand M, Finney JL, Daniel RM, Smith JC. Solvent dependence of dynamic transitions in protein solutions. Proceedings of the National Academy of Sciences of the United States of America. 97: 9961-6. PMID 10963663  0.48
2000 Réat V, Finney JL, Steer A, Roberts MA, Smith J, Dunn R, Peterson M, Daniel R. Cryosolvents useful for protein and enzyme studies below -100 degrees C. Journal of Biochemical and Biophysical Methods. 42: 97-103. PMID 10737214 DOI: 10.1016/S0165-022X(99)00053-6  0.48
1999 Daniel RM, Finney JL, Réat V, Dunn R, Ferrand M, Smith JC. Enzyme dynamics and activity: time-scale dependence of dynamical transitions in glutamate dehydrogenase solution. Biophysical Journal. 77: 2184-90. PMID 10512837 DOI: 10.1016/S0006-3495(99)77058-X  0.48
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  1
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  0.4
1998 MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FT, Mattos C, ... ... Smith JC, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. The Journal of Physical Chemistry. B. 102: 3586-616. PMID 24889800 DOI: 10.1021/jp973084f  1
1998 Daniel RM, Smith JC, Ferrand M, Héry S, Dunn R, Finney JL. Enzyme activity below the dynamical transition at 220 K. Biophysical Journal. 75: 2504-7. PMID 9788945 DOI: 10.1016/S0006-3495(98)77694-5  0.48
1998 Bellissent-Funel MC, Daniel R, Durand D, Ferrand M, Finney JL, Pouget S, Reat V, Smith JC. Nanosecond protein dynamics: First detection of a neutron incoherent spin-echo signal [1] Journal of the American Chemical Society. 120: 7347-7348. DOI: 10.1021/ja981329b  1
1997 Petrescu AJ, Receveur V, Calmettes P, Durand D, Desmadril M, Roux B, Smith JC. Small-angle neutron scattering by a strongly denatured protein: analysis using random polymer theory. Biophysical Journal. 72: 335-42. PMID 8994618 DOI: 10.1016/S0006-3495(97)78672-7  1
1996 Roux B, Nina M, Pomès R, Smith JC. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophysical Journal. 71: 670-81. PMID 8842206 DOI: 10.1016/S0006-3495(96)79267-6  1
1995 Nina M, Roux B, Smith JC. Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water. Biophysical Journal. 68: 25-39. PMID 7711248 DOI: 10.1016/S0006-3495(95)80184-0  1
1993 Calmettes P, Roux B, Durand D, Desmadril M, Smith JC. Configurational distribution of denatured phosphoglycerate kinase. Journal of Molecular Biology. 231: 840-8. PMID 8515454  1
1993 Thomas A, Roux B, Smith JC. Computer simulations of the flexibility of a series of synthetic cyclic peptide analogues. Biopolymers. 33: 1249-70. PMID 8364158 DOI: 10.1002/bip.360330811  1
1993 Ferrand M, Zaccai G, Nina M, Smith JC, Etchebest C, Roux B. Structure and dynamics of bacteriorhodopsin. Comparison of simulation and experiment. Febs Letters. 327: 256-60. PMID 8348952  1
1992 Moeller KD, Williams GP, Steinhauser S, Hirschmugl C, Smith JC. Hydration-dependent far-infrared absorption in lysozyme detected using synchrotron radiation Biophysical Journal. 61: 276-280. PMID 1540696 DOI: 10.1016/S0006-3495(92)81834-9  1
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