Jeremy C. Smith - Publications

Affiliations: 
Molecular Biophysics Oak Ridge National Laboratory, Oak Ridge, TN, United States 
Website:
http://cmb.ornl.gov/people/smith

279 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
2022 Glaser J, Sedova A, Galanie S, Kneller DW, Davidson RB, Maradzike E, Del Galdo S, Labbé A, Hsu DJ, Agarwal R, Bykov D, Tharrington A, Parks JM, Smith DMA, Daidone I, ... ... Smith JC, et al. Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor. Acs Pharmacology & Translational Science. 5: 255-265. PMID 35434531 DOI: 10.1021/acsptsci.2c00026  0.786
2021 Gumbart JC, Ferreira JL, Hwang H, Hazel AJ, Cooper CJ, Parks JM, Smith JC, Zgurskaya HI, Beeby M. Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump. Biophysical Journal. PMID 34411576 DOI: 10.1016/j.bpj.2021.08.016  0.535
2021 Zanetti-Polzi L, Smith MD, Chipot C, Gumbart JC, Lynch DL, Pavlova A, Smith JC, Daidone I. Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design. The Journal of Physical Chemistry Letters. 4195-4202. PMID 33900080 DOI: 10.1021/acs.jpclett.1c00425  0.513
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  0.559
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  0.739
2020 Acharya A, Agarwal R, Baker M, Baudry J, Bhowmik D, Boehm S, Byler K, Coates L, Chen SY, Cooper CJ, Demerdash O, Daidone I, Eblen J, Ellingson SR, Forli S, ... ... Smith JC, et al. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. Chemrxiv : the Preprint Server For Chemistry. PMID 33200117 DOI: 10.26434/chemrxiv.12725465.v1  0.774
2020 Zanetti-Polzi L, Smith M, Chipot C, Gumbart JC, Lynch DL, Pavlova A, Smith JC, Daidone I. Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design. Chemrxiv : the Preprint Server For Chemistry. PMID 33200115 DOI: 10.26434/chemrxiv.13200227  0.519
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  0.315
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  0.54
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  0.639
2020 LeGrand S, Scheinberg A, Tillack AF, Thavappiragasam M, Vermaas JV, Agarwal R, Larkin J, Poole D, Santos-Martins D, Solis-Vasquez L, Koch A, Forli S, Hernandez O, Smith JC, Sedova A. GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research. Arxiv. PMID 32676519  0.776
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  0.314
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  0.349
2020 Parks JM, Smith JC. How to Discover Antiviral Drugs Quickly. The New England Journal of Medicine. PMID 32433861 DOI: 10.1056/Nejmcibr2007042  0.308
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  0.329
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  0.594
2020 Gumbart JC, Ferreira J, hwang S, Hazel A, Parks JM, Smith JC, Beeby M, Zgurskaya H. Modeling the Placement of the AcrAB-TolC Multidrug Efflux Pump in the Bacterial Cell Envelope Biophysical Journal. 118: 13a. DOI: 10.1016/J.Bpj.2019.11.251  0.521
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  0.738
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  0.614
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  0.396
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  0.602
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  0.623
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  0.345
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  0.324
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  0.808
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  0.571
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  0.617
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  0.308
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  0.325
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  0.741
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  0.624
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  0.682
2018 Vural D, Smith JC, Glyde HR. Determination of Dynamical Heterogeneity from Dynamic Neutron-Scattering of Proteins. Biophysical Journal. PMID 29580551 DOI: 10.1016/J.Bpj.2018.02.024  0.349
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  0.336
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  0.74
2018 Kovalevsky A, Aggarwal M, Velazquez H, Cuneo MJ, Blakeley MP, Weiss KL, Smith JC, Fisher SZ, McKenna R. "To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation. Structure (London, England : 1993). PMID 29429876 DOI: 10.1016/J.Str.2018.01.006  0.326
2018 Devarajan D, Lian P, Brooks SC, Parks JM, Smith JC. Quantum Chemical Approach for Calculating Stability Constants of Mercury Complexes Acs Earth and Space Chemistry. 2: 1168-1178. DOI: 10.1021/Acsearthspacechem.8B00102  0.629
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  0.732
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  0.378
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  0.598
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  0.64
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  0.312
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  0.622
2017 Bondar AN, Smith JC. Protonation-state Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins. Photochemistry and Photobiology. PMID 28477350 DOI: 10.1111/Php.12790  0.342
2017 Smith JC. Pickin' Up Good Vibrations. Biophysical Journal. 112: 829-830. PMID 28297641 DOI: 10.1016/J.Bpj.2017.01.008  0.333
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  0.304
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. PMID 28461893 DOI: 10.1107/S2052252516010514  0.308
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  0.562
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  0.596
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  0.605
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  0.361
2016 Simakov NA, Leonard DA, Smith JC, Wymore T, Szarecka A. A Distal Disulfide Bridge in OXA-1 β-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of Specificity Determining Ω Loop. The Journal of Physical Chemistry. B. PMID 27668669 DOI: 10.1021/Acs.Jpcb.6B07884  0.338
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  0.766
2016 Parks JM, Smith JC. Modeling Mercury in Proteins. Methods in Enzymology. 578: 103-22. PMID 27497164 DOI: 10.1016/Bs.Mie.2016.05.041  0.322
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  0.308
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  0.301
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  0.371
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  0.732
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  0.305
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  0.711
2016 Petridis L, Smith JC. Conformations of Low-Molecular-Weight Lignin Polymers in Water. Chemsuschem. PMID 26763657 DOI: 10.1002/Cssc.201501350  0.303
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  0.325
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  0.322
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  0.314
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  0.735
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  0.318
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  0.686
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  0.354
2015 Topham CM, Smith JC. Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues. Computational Biology and Chemistry. 54: 33-43. PMID 25544680 DOI: 10.1016/J.Compbiolchem.2014.11.007  0.342
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  0.806
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  0.303
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  0.798
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  0.326
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  0.303
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  0.712
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  0.389
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  0.34
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  0.344
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  0.348
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  0.361
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  0.321
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  0.764
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  0.586
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  0.35
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  0.768
2014 Langan P, Petridis L, O'Neill HM, Pingali SV, Foston M, Nishiyama Y, Schulz R, Lindner B, Leif Hanson B, Harton S, Heller WT, Urban V, Evans BR, Gnanakaran S, Ragauskas AJ, ... Smith JC, et al. Common processes drive the thermochemical pretreatment of lignocellulosic biomass Green Chemistry. 16: 63-68. DOI: 10.1039/C3Gc41962B  0.304
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  0.705
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  0.395
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  0.343
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  0.547
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  0.63
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  0.618
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  0.518
2013 Godec A, Smith JC, Merzel F. Soft collective fluctuations governing hydrophobic association. Physical Review Letters. 111: 127801. PMID 24093302 DOI: 10.1103/Physrevlett.111.127801  0.315
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  0.304
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  0.31
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  0.391
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  0.771
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  0.629
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  0.34
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  0.376
2013 Hong L, Glass DC, Nickels JD, Perticaroli S, Yi Z, Tyagi M, O’Neill H, Zhang Q, Sokolov AP, Smith JC. Publisher’s Note: Elastic and Conformational Softness of a Globular Protein [Phys. Rev. Lett.110, 028104 (2013)] Physical Review Letters. 110. DOI: 10.1103/Physrevlett.110.069901  0.317
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  0.675
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  0.654
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  0.357
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  0.312
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  0.319
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  0.313
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  0.323
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  0.313
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  0.666
2012 Smolin N, Biehl R, Kneller GR, Richter D, Smith JC. Functional domain motions in proteins on the ~1-100 ns timescale: comparison of neutron spin-echo spectroscopy of phosphoglycerate kinase with molecular-dynamics simulation. Biophysical Journal. 102: 1108-17. PMID 22404933 DOI: 10.1016/J.Bpj.2012.01.002  0.363
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  0.327
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  0.33
2012 Langan P, Evans BR, Foston M, Heller WT, O'Neill H, Petridis L, Pingali SV, Ragauskas AJ, Smith JC, Urban VS, Davison BH. Neutron technologies for bioenergy research Industrial Biotechnology. 8: 209-216. DOI: 10.1089/Ind.2012.0012  0.305
2012 Lindner B, Smith JC. Sassena — X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers Computer Physics Communications. 183: 1491-1501. DOI: 10.1016/J.Cpc.2012.02.010  0.331
2012 Ulmschneider JP, White SH, Smith J, Ulmschneider MB. The Difference Between Translocon-Assisted Membrane Insertion and Free Surface-To-Bilayer Peptide Insertion Biophysical Journal. 102: 615a. DOI: 10.1016/J.Bpj.2011.11.3355  0.307
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  0.666
2012 Sangha AK, Petridis L, Smith JC, Ziebell A, Parks JM. Molecular simulation as a tool for studying lignin Environmental Progress and Sustainable Energy. 31: 47-54. DOI: 10.1002/Ep.10628  0.307
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  0.359
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 DOI: 10.1103/Physrevlett.107.148102  0.393
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  0.301
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  0.317
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  0.344
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  0.338
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  0.319
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  0.356
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  0.581
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  0.324
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  0.586
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  0.585
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 DOI: 10.1103/Physreve.83.021902  0.79
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  0.628
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  0.613
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  0.307
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  0.57
2011 Petridis L, Pingali SV, Urban V, Heller WT, O’Neill HM, Foston M, Ragauskas A, Smith JC. Publisher’s Note: Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation [Phys. Rev. E83, 061911 (2011)] Physical Review E. 84. DOI: 10.1103/Physreve.84.019905  0.349
2011 Johs A, Parks JM, Harwood I, Guo H, Smith J, Miller SM, Summers AO, Liang L. Biomolecular Mechanisms of Microbial Mercury Resistance in the Environment Biophysical Journal. 100: 313a. DOI: 10.1016/J.Bpj.2010.12.1910  0.325
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  0.646
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  0.449
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  0.566
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  0.327
2010 Xu J, Smith JC. Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin-dockerin complex and its variants. Protein Engineering, Design & Selection : Peds. 23: 759-68. PMID 20682763 DOI: 10.1093/Protein/Gzq049  0.338
2010 Ulmschneider MB, Smith JC, Ulmschneider JP. Peptide partitioning properties from direct insertion studies. Biophysical Journal. 98: L60-2. PMID 20550886 DOI: 10.1016/J.Bpj.2010.03.043  0.334
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  0.33
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  0.319
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  0.318
2010 Moritsugu K, Njunda BM, Smith JC. Theory and normal-mode analysis of change in protein vibrational dynamics on ligand binding. The Journal of Physical Chemistry. B. 114: 1479-85. PMID 20043649 DOI: 10.1021/Jp909677P  0.344
2010 Glass DC, Krishnan M, Nutt DR, Smith JC. Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models Journal of Chemical Theory and Computation. 6: 1390-1400. DOI: 10.1021/Ct9006508  0.371
2010 Splettstoesser T, Holmes KC, Noé F, Smith JC. A Comparison of Actin Filament Models by Molecular Dynamics Simulation Biophysical Journal. 98: 154a. DOI: 10.1016/J.Bpj.2009.12.826  0.569
2010 Alekozai EM, Cheng X, Smith JC. Analysis of the Cellulose-Cellulase Interaction Biophysical Journal. 98: 433a. DOI: 10.1016/J.Bpj.2009.12.2347  0.3
2010 Smolin N, Lindner B, Guo H, Smith JC. Integration of Computer Simulation and Neutron Scattering in the Characterization of Protein Dynamics Biophysical Journal. 98: 237a. DOI: 10.1016/J.Bpj.2009.12.1282  0.385
2010 Thukral L, Smith JC, Daidone I. Common Folding Mechanism of a Peptide Revealed by Multiple MD Simulations Biophysical Journal. 98: 199a-200a. DOI: 10.1016/J.Bpj.2009.12.1065  0.35
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  0.329
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  0.339
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  0.338
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  0.455
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  0.468
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  0.405
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  0.319
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 DOI: 10.1103/Physreve.80.011109  0.77
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  0.321
2009 Phatak P, Frähmcke JS, Wanko M, Hoffmann M, Strodel P, Smith JC, Suhai S, Bondar AN, Elstner M. Long-distance proton transfer with a break in the bacteriorhodopsin active site. Journal of the American Chemical Society. 131: 7064-78. PMID 19405533 DOI: 10.1021/Ja809767V  0.303
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  0.369
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  0.321
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  0.556
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  0.336
2009 Lopez M, Kurkal-Siebert V, Dunn R, Tehei M, Finney J, Smith J, Daniel R. Enzyme activity and dynamics in near-anhydrous conditions Nature Precedings. 4: 1-1. DOI: 10.1038/Npre.2009.3884.1  0.57
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  0.64
2008 Nutt DR, Smith JC. Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations. Journal of the American Chemical Society. 130: 13066-73. PMID 18774821 DOI: 10.1021/Ja8034027  0.339
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  0.596
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 DOI: 10.1103/Physrevlett.100.188103  0.788
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  0.387
2008 Moritsugu K, Smith JC. REACH coarse-grained biomolecular simulation: transferability between different protein structural classes. Biophysical Journal. 95: 1639-48. PMID 18469078 DOI: 10.1529/Biophysj.108.131714  0.377
2008 Krishnan M, Kurkal-Siebert V, Smith JC. Methyl group dynamics and the onset of anharmonicity in myoglobin. The Journal of Physical Chemistry. B. 112: 5522-33. PMID 18399677 DOI: 10.1021/Jp076641Z  0.36
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  0.585
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  0.347
2007 Nutt DR, Smith JC. Molecular Dynamics Simulations of Proteins:  Can the Explicit Water Model Be Varied? Journal of Chemical Theory and Computation. 3: 1550-60. PMID 26633225 DOI: 10.1021/Ct700053U  0.338
2007 Meinhold L, Smith JC, Kitao A, Zewail AH. Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation. Proceedings of the National Academy of Sciences of the United States of America. 104: 17261-5. PMID 17956984 DOI: 10.1073/Pnas.0708199104  0.341
2007 Meinhold L, Merzel F, Smith JC. Lattice dynamics of a protein crystal Physical Review Letters. 99: 138101. PMID 17930640 DOI: 10.1103/Physrevlett.99.138101  0.338
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  0.334
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  0.358
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  0.61
2007 Meinhold L, Smith JC. Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns. Proteins. 66: 941-53. PMID 17154425 DOI: 10.1002/Prot.21246  0.333
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  0.647
2007 Moritsugu K, Smith JC. Langevin model of the temperature and hydration dependence of protein vibrational dynamics. The Journal of Physical Chemistry. B. 109: 12182-94. PMID 16852503 DOI: 10.1021/Jp044272Q  0.321
2007 Gräter F, Schwarzl SM, Dejaegere A, Fischer S, Smith JC. Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics. The Journal of Physical Chemistry. B. 109: 10474-83. PMID 16852269 DOI: 10.1021/Jp044185Y  0.31
2007 Moritsugu K, Smith JC. Temperature-dependent protein dynamics: a simulation-based probabilistic diffusion-vibration Langevin description. The Journal of Physical Chemistry. B. 110: 5807-16. PMID 16539528 DOI: 10.1021/Jp055314T  0.357
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  0.546
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  0.576
2006 Bondar AN, Suhai S, Fischer S, Smith JC, Elstner M. Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: a theoretical analysis of structural elements. Journal of Structural Biology. 157: 454-69. PMID 17189704 DOI: 10.1016/J.Jsb.2006.10.007  0.31
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  0.614
2006 Topham CM, Smith JC. Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form. Biophysical Journal. 92: 769-86. PMID 17071666 DOI: 10.1529/Biophysj.105.079723  0.318
2006 Bondar AN, Smith JC, Fischer S. Structural and energetic determinants of primary proton transfer in bacteriorhodopsin. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society For Photobiology. 5: 547-52. PMID 16761083 DOI: 10.1039/B516451F  0.306
2006 Mesentean S, Fischer S, Smith JC. Analyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mapping. Proteins. 64: 210-8. PMID 16617427 DOI: 10.1002/Prot.20981  0.3
2006 Kurkal-Siebert V, Smith JC. Low-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 k. Journal of the American Chemical Society. 128: 2356-64. PMID 16478191 DOI: 10.1021/Ja055962Q  0.396
2006 Merzel F, Smith JC. High-density hydration layer of lysozymes: molecular dynamics decomposition of solution scattering data. Journal of Chemical Information and Modeling. 45: 1593-9. PMID 16309259 DOI: 10.1021/Ci0502000  0.323
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  0.59
2006 Sengupta D, Meinhold L, Langosch D, Ullmann GM, Smith JC. Understanding the energetics of helical peptide orientation in membranes. Proteins. 58: 913-22. PMID 15657932 DOI: 10.1002/Prot.20383  0.31
2006 Noé F, Oswald M, Reinelt G, Fischer S, Smith JC. Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the AlphaL \leftrightharpoons Beta \leftrightharpoons AlphaR Transitions in Octaalanine Multiscale Modeling & Simulation. 5: 393-419. DOI: 10.1137/050641922  0.565
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  0.579
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  0.602
2005 Meinhold L, Smith JC. Pressure-dependent transition in protein dynamics at about revealed by molecular dynamics simulation. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 061908. PMID 16485975 DOI: 10.1103/Physreve.72.061908  0.354
2005 Meinhold L, Smith JC. Correlated dynamics determining x-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation. Physical Review Letters. 95: 218103. PMID 16384188 DOI: 10.1103/Physrevlett.95.218103  0.379
2005 Cournia Z, Smith JC, Ullmann GM. A molecular mechanics force field for biologically important sterols. Journal of Computational Chemistry. 26: 1383-99. PMID 16028234 DOI: 10.1002/Jcc.20277  0.348
2005 Schwarzl SM, Huang D, Smith JC, Fischer S. Nonuniform charge scaling (NUCS): a practical approximation of solvent electrostatic screening in proteins. Journal of Computational Chemistry. 26: 1359-71. PMID 16021598 DOI: 10.1002/Jcc.20274  0.353
2005 Sengupta D, Behera RN, Smith JC, Ullmann GM. The alpha helix dipole: screened out? Structure (London, England : 1993). 13: 849-55. PMID 15939016 DOI: 10.1016/J.Str.2005.03.010  0.325
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  0.577
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  0.596
2005 Bondar AN, Elstner M, Suhai S, Smith JC, Fischer S. Mechanism of primary proton transfer in bacteriorhodopsin. Structure (London, England : 1993). 12: 1281-8. PMID 15242604 DOI: 10.1016/J.Str.2004.04.016  0.302
2005 Hammel M, Fierobe H, Czjzek M, Kurkal V, Smith JC, Bayer EA, Finet S, Receveur-Bréchot V. Structural Basis of Cellulosome Efficiency Explored by Small Angle X-ray Scattering Journal of Biological Chemistry. 280: 38562-38568. DOI: 10.1074/Jbc.M503168200  0.347
2005 Kurkal V, Daniel RM, Finney JL, Tehei M, Dunn RV, Smith JC. Low frequency enzyme dynamics as a function of temperature and hydration: A neutron scattering study Chemical Physics. 317: 267-273. DOI: 10.1016/J.Chemphys.2005.05.019  0.596
2004 Bondar AN, Fischer S, Smith JC, Elstner M, Suhai S. Key role of electrostatic interactions in bacteriorhodopsin proton transfer. Journal of the American Chemical Society. 126: 14668-77. PMID 15521787 DOI: 10.1021/Ja047982I  0.314
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  0.614
2004 Balog E, Becker T, Oettl M, Lechner R, Daniel R, Finney J, Smith JC. Direct determination of vibrational density of states change on ligand binding to a protein. Physical Review Letters. 93: 028103. PMID 15323955 DOI: 10.1103/Physrevlett.93.028103  0.567
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  0.34
2004 Vaiana AC, Neuweiler H, Schulz A, Wolfrum J, Sauer M, Smith JC. Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation. Journal of the American Chemical Society. 125: 14564-72. PMID 14624606 DOI: 10.1021/Ja036082J  0.302
2004 Bondar N, Elstner M, Fischer S, Smith JC, Suhai S. Can coordinate driving describe proton transfer coupled to complex protein motions Phase Transitions. 77: 47-52. DOI: 10.1080/01411590310001622455  0.31
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  0.536
2003 Tournier AL, Smith JC. Principal components of the protein dynamical transition. Physical Review Letters. 91: 208106. PMID 14683404 DOI: 10.1103/Physrevlett.91.208106  0.357
2003 Mihailescu D, Reed J, Smith JC. Convergence in peptide folding simulation: multiple trajectories of a potential AIDS pharmacophore. Biopolymers. 70: 121-33. PMID 14517902 DOI: 10.1002/Bip.10401  0.357
2003 Tournier AL, Xu J, Smith JC. Translational hydration water dynamics drives the protein glass transition. Biophysical Journal. 85: 1871-5. PMID 12944299 DOI: 10.1016/S0006-3495(03)74614-1  0.382
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  0.61
2003 Becker T, Smith JC. Energy resolution and dynamical heterogeneity effects on elastic incoherent neutron scattering from molecular systems. Physical Review E. 67: 21904. PMID 12636712 DOI: 10.1103/Physreve.67.021904  0.349
2003 Vaiana AC, Schulz A, Wolfrum J, Sauer M, Smith JC. Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching. Journal of Computational Chemistry. 24: 632-9. PMID 12632478 DOI: 10.1002/Jcc.10190  0.304
2003 Gruia AD, Fischer S, Smith JC. Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease. Proteins. 50: 507-15. PMID 12557192 DOI: 10.1002/Prot.10312  0.37
2003 Tournier AL, Huang D, Schwarzl SM, Fischer S, Smith JC. Time-resolved computational protein biochemistry: solvent effects on interactions, conformational transitions and equilibrium fluctuations. Faraday Discussions. 122: 243-51; discussion 2. PMID 12555861 DOI: 10.1039/B201191C  0.385
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 DOI: 10.1039/B200989G  0.605
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  0.588
2003 Huynh T, Smith JC, Sanson A. Protein unfolding transitions in an intrinsically unstable annexin domain: molecular dynamics simulation and comparison with nuclear magnetic resonance data. Biophysical Journal. 83: 681-98. PMID 12124256 DOI: 10.1016/S0006-3495(02)75200-4  0.319
2003 Kataoka M, Kamikubo H, Nakagawa H, Parker SF, Smith JC. Neutron inelastic scattering as a high-resolution vibrational spectroscopy: New tool for the study of protein dynamics Spectroscopy. 17: 529-535. DOI: 10.1155/2003/907042  0.369
2003 Tournier AL, Xu J, Smith JC. Solvent caging of internal motions in myoglobin at low temperaturesThis paper was originally presented as a poster at the Faraday Discussion 122 meeting. Physchemcomm. 6: 6-8. DOI: 10.1039/B209839C  0.375
2003 Hayward JA, Daniel RM, Finney JL, Smith JC. Use of computer simulation in the interpretation of elastic neutron scattering in complex molecular systems: A small protein in various environments Chemical Physics. 292: 389-396. DOI: 10.1016/S0301-0104(03)00080-6  0.63
2002 Schwarzl SM, Tschopp TB, Smith JC, Fischer S. Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction? Journal of Computational Chemistry. 23: 1143-9. PMID 12116383 DOI: 10.1002/Jcc.10112  0.312
2002 Merzel F, Smith JC. Is the first hydration shell of lysozyme of higher density than bulk water Proceedings of the National Academy of Sciences of the United States of America. 99: 5378-5383. PMID 11959992 DOI: 10.1073/Pnas.082335099  0.337
2002 Hayward JA, Smith JC. Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties. Biophysical Journal. 82: 1216-25. PMID 11867439 DOI: 10.1016/S0006-3495(02)75478-7  0.412
2002 Mihailescu D, Smith JC, Reed J. Solution structure of a putative HIV1 immunogenic peptide: computer simulation of the principal CD4 binding domain of gp120. Journal of Medicinal Chemistry. 45: 1019-25. PMID 11855981 DOI: 10.1021/Jm0109715  0.317
2002 Merzel F, Smith JC. SASSIM: a method for calculating small‐angle X‐ray and neutron scattering and the associated molecular envelope from explicit‐atom models of solvated proteins Acta Crystallographica Section D-Biological Crystallography. 58: 242-249. PMID 11807248 DOI: 10.1107/S0907444901019576  0.354
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 DOI: 10.1073/Pnas.97.18.9961  0.608
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  0.557
2000 DUNN RV, RÉAT V, FINNEY J, FERRAND M, SMITH JC, DANIEL RM. Enzyme activity and dynamics: xylanase activity in the absence of fast anharmonic dynamics Biochemical Journal. 346: 355-358. DOI: 10.1042/Bj3460355  0.563
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  0.588
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  0.736
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  0.696
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  0.768
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  0.592
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  0.54
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  0.574
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  0.73
1996 Svensson B, Etchebest C, Tuffery P, van Kan P, Smith J, Styring S. A model for the photosystem II reaction center core including the structure of the primary donor P680. Biochemistry. 35: 14486-502. PMID 8931545 DOI: 10.1021/Bi960764K  0.301
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  0.714
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  0.584
1995 Foloppe N, Ferrand M, Breton J, Smith JC. Structural model of the photosynthetic reaction center of Rhodobacter capsulatus. Proteins. 22: 226-44. PMID 7479696 DOI: 10.1002/Prot.340220304  0.351
1995 Micu AM, Durand D, Quilichini M, Field MJ, Smith JC. Collective Vibrations in Crystalline L-Alanine. [Erratum to document cited in CA122:291480] The Journal of Physical Chemistry. 99: 13052-13052. DOI: 10.1021/J100034A056  0.529
1995 Micu AM, Durand D, Quilichini M, Field MJ, Smith JC. Collective Vibrations in Crystalline L-Alanine The Journal of Physical Chemistry. 99: 5645-5657. DOI: 10.1021/J100015A057  0.536
1994 Faure P, Micu A, Pérahia D, Doucet J, Smith JC, Benoit JP. Correlated intramolecular motions and diffuse x-ray scattering in lysozyme Nature Structural Biology. 1: 124-128. PMID 7656016 DOI: 10.1038/Nsb0294-124  0.583
1994 Smith JC. Protein interactions and dynamics probed by quantum chemistry, computer simulations and neutron experiments Biophysical Chemistry. 53: 131-143. DOI: 10.1016/0301-4622(94)00084-0  0.41
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  0.627
1994 Nardi F, Doster W, Tidor B, Karplus M, Cusack S, Smith J. Dynamics of tRNA: Experimental Neutron Spectra Compared with a Normal Mode Analysis Israel Journal of Chemistry. 34: 233-238. DOI: 10.1002/Ijch.199400026  0.743
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 DOI: 10.1006/Jmbi.1993.1330  0.609
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  0.615
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 DOI: 10.1016/0014-5793(93)80999-B  0.631
1993 Durand D, Field MJ, Quilichini M, Smith JC. Lattice vibrations in crystalline L-alanine. Biopolymers. 33: 725-33. PMID 8343574 DOI: 10.1002/Bip.360330502  0.584
1993 Nina M, Smith J, Roux B. Ab initio quantum chemical analysis of Schiff base-water interactions in bacteriorhodopsin Journal of Molecular Structure: Theochem. 286: 231-245. DOI: 10.1016/0166-1280(93)87166-B  0.587
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  0.318
1992 Kneller GR, Doster W, Settles M, Cusack S, Smith JC. Methyl group dynamics in the crystalline alanine dipeptide: A combined computer simulation and inelastic neutron scattering analysis The Journal of Chemical Physics. 97: 8864-8879. DOI: 10.1063/1.463361  0.579
1992 Smith JC, Karplus M. Empirical force field study of geometries and conformational transitions of some organic molecules Journal of the American Chemical Society. 114: 801-812. DOI: 10.1021/Ja00029A001  0.532
1992 Velikson B, Garel T, Niel J-, Orland H, Smith J. Conformational distribution of heptaalanine: Analysis using a new Monte Carlo chain growth method Journal of Computational Chemistry. 13: 1216-1233. DOI: 10.1002/Jcc.540131006  0.326
1991 Smith JC. Protein dynamics: Comparison of simulations with inelastic neutron scattering experiments Quarterly Reviews of Biophysics. 24: 227-291. PMID 1749823 DOI: 10.1017/S0033583500003723  0.377
1991 Garen J, Field M, Kneller G, Karplus M, Smith J. Torsional motions of methyl and ammonium groups in the L-alanine crystal : a comparison of molecular dynamics and normal mode calculations Journal De Chimie Physique. 88: 2587-2596. DOI: 10.1051/Jcp/1991882587  0.703
1991 Garel T, Niel J, Orland H, Smith J, Velikson B. Comparison of a new Monte Carlo peptide conformational search procedure with high temperature molecular dynamics Journal De Chimie Physique. 88: 2479-2488. DOI: 10.1051/Jcp/1991882479  0.364
1990 Smith J, Kuczera K, Karplus M. Dynamics of myoglobin: Comparison of simulation results with neutron scattering spectra Proceedings of the National Academy of Sciences of the United States of America. 87: 1601-1605. PMID 2304919 DOI: 10.1073/Pnas.87.4.1601  0.593
1990 Smith J, Cusack S, Tidor B, Karplus M. Inelastic neutron scattering analysis of low‐frequency motions in proteins: Harmonic and damped harmonic models of bovine pancreatic tryspin inhibitor The Journal of Chemical Physics. 93: 2974-2991. DOI: 10.1063/1.458885  0.734
1989 Smith J, Kuczera K, Tidor B, Doster W, Cusack S, Karplus M. Internal dynamics of globular proteins: Comparison of neutron scattering measurements and theoretical models Physica B: Physics of Condensed Matter. 156: 437-443. DOI: 10.1016/0921-4526(89)90699-6  0.757
1988 Cusack S, Smith J, Finney J, Tidor B, Karplus M. Inelastic neutron scattering analysis of picosecond internal protein dynamics. Comparison of harmonic theory with experiment. Journal of Molecular Biology. 202: 903-8. PMID 2459399 DOI: 10.1016/0022-2836(88)90566-9  0.752
1987 Smith J, Cusack S, Poole P, Finney J. Direct measurement of hydration-related dynamic changes in lysozyme using inelastic neutron scattering spectroscopy. Journal of Biomolecular Structure & Dynamics. 4: 583-588. PMID 3271457 DOI: 10.1080/07391102.1987.10507662  0.674
1986 Smith J, Cusack S, Pezzeca U, Brooks B, Karplus M. Inelastic neutron scattering analysis of low frequency motion in proteins: A normal mode study of the bovine pancreatic trypsin inhibitor The Journal of Chemical Physics. 85: 3636-3654. DOI: 10.1063/1.450935  0.728
1986 Cusack S, Smith J, Finney J, Karplus M, Trewhella J. Low frequency dynamics of proteins studied by neutron time-of-flight spectroscopy Physica B+C. 136: 256-259. DOI: 10.1016/S0378-4363(86)80069-9  0.649
1986 Cusack S, Smith J, Finney J, Karplus M, Trewhella J. Low frequency dynamics of proteins studied by neutron time-of-flight spectroscopy Physica B+C. 136: 256-259. DOI: 10.1016/S0378-4363(86)80069-9  0.69
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