Статті в журналах з теми "QM/MM simulations"
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Suh, Donghyuk, Kwangho Nam, and Wonpil Im. "CHARMM-GUI QM/MM interfacer for the hybrid QM/MM molecular dynamics simulations." Biophysical Journal 122, no. 3 (February 2023): 424a. http://dx.doi.org/10.1016/j.bpj.2022.11.2299.
Повний текст джерелаKulkarni, Prajakta U., Harshil Shah, and Vivek K. Vyas. "Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-Based Drug Design and Discovery." Mini-Reviews in Medicinal Chemistry 22, no. 8 (May 2022): 1096–107. http://dx.doi.org/10.2174/1389557521666211007115250.
Повний текст джерелаWatanabe, Hiroshi C., and Qiang Cui. "Quantitative Analysis of QM/MM Boundary Artifacts and Correction in Adaptive QM/MM Simulations." Journal of Chemical Theory and Computation 15, no. 7 (May 16, 2019): 3917–28. http://dx.doi.org/10.1021/acs.jctc.9b00180.
Повний текст джерелаde la Lande, Aurélien, Aurelio Alvarez-Ibarra, Karim Hasnaoui, Fabien Cailliez, Xiaojing Wu, Tzonka Mineva, Jérôme Cuny, et al. "Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review." Molecules 24, no. 9 (April 26, 2019): 1653. http://dx.doi.org/10.3390/molecules24091653.
Повний текст джерелаKönig, Gerhard, Frank Pickard, Jing Huang, Walter Thiel, Alexander MacKerell, Bernard Brooks, and Darrin York. "A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes." Molecules 23, no. 10 (October 19, 2018): 2695. http://dx.doi.org/10.3390/molecules23102695.
Повний текст джерелаLiang, Dongyue, Jiewei Hong, Dong Fang, Joseph W. Bennett, Sara E. Mason, Robert J. Hamers, and Qiang Cui. "Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations." Physical Chemistry Chemical Physics 20, no. 5 (2018): 3349–62. http://dx.doi.org/10.1039/c7cp06709g.
Повний текст джерелаYang, Wei, Ryan Bitetti-Putzer, and Martin Karplus. "Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials." Journal of Chemical Physics 120, no. 20 (May 22, 2004): 9450–53. http://dx.doi.org/10.1063/1.1738106.
Повний текст джерелаChalmet, S., D. Rinaldi, and M. F. Ruiz-López. "A QM/MM/continuum model for computations in solution: Comparison with QM/MM molecular dynamics simulations." International Journal of Quantum Chemistry 84, no. 5 (2001): 559–64. http://dx.doi.org/10.1002/qua.1410.
Повний текст джерелаShimada, J., T. Sakuma, K. Nakata, T. Wasiho, and T. Takada. "3K1015 BioMolecular Simulations : MD and QM/MM calculations." Seibutsu Butsuri 42, supplement2 (2002): S180. http://dx.doi.org/10.2142/biophys.42.s180_2.
Повний текст джерелаSolt, Iván, Petr Kulhánek, István Simon, Steven Winfield, Mike C. Payne, Gábor Csányi, and Monika Fuxreiter. "Evaluating Boundary Dependent Errors in QM/MM Simulations." Journal of Physical Chemistry B 113, no. 17 (April 30, 2009): 5728–35. http://dx.doi.org/10.1021/jp807277r.
Повний текст джерелаMorzan, Uriel N., Diego J. Alonso de Armiño, Nicolás O. Foglia, Francisco Ramírez, Mariano C. González Lebrero, Damián A. Scherlis, and Darío A. Estrin. "Spectroscopy in Complex Environments from QM–MM Simulations." Chemical Reviews 118, no. 7 (March 21, 2018): 4071–113. http://dx.doi.org/10.1021/acs.chemrev.8b00026.
Повний текст джерелаMartins Costa, M. T. C. "QM/MM simulations of polyols in aqueous solution." Journal of Molecular Structure: THEOCHEM 729, no. 1-2 (September 2005): 47–52. http://dx.doi.org/10.1016/j.theochem.2005.03.016.
Повний текст джерелаJász, Ádám, Ádám Rák, István Ladjánszki, Gábor János Tornai, and György Cserey. "Towards chemically accurate QM/MM simulations on GPUs." Journal of Molecular Graphics and Modelling 96 (May 2020): 107536. http://dx.doi.org/10.1016/j.jmgm.2020.107536.
Повний текст джерелаRiahi, Saleh, and Christopher N. Rowley. "QM/MM Simulations of Mg and Zn Solvation." Biophysical Journal 106, no. 2 (January 2014): 405a. http://dx.doi.org/10.1016/j.bpj.2013.11.2281.
Повний текст джерелаDohm, Sebastian, Eckhard Spohr, and Martin Korth. "Developing adaptive QM/MM computer simulations for electrochemistry." Journal of Computational Chemistry 38, no. 1 (October 28, 2016): 51–58. http://dx.doi.org/10.1002/jcc.24513.
Повний текст джерелаDoll, K., and T. Jacob. "QM/MM description of periodic systems." Journal of Theoretical and Computational Chemistry 14, no. 07 (November 2015): 1550054. http://dx.doi.org/10.1142/s0219633615500546.
Повний текст джерелаMiranda, Sebastião, Jonas Feldt, Frederico Pratas, Ricardo A. Mata, Nuno Roma, and Pedro Tomás. "Efficient parallelization of perturbative Monte Carlo QM/MM simulations in heterogeneous platforms." International Journal of High Performance Computing Applications 31, no. 6 (July 27, 2016): 499–516. http://dx.doi.org/10.1177/1094342016649420.
Повний текст джерелаTzeliou, Christina Eleftheria, Markella Aliki Mermigki, and Demeter Tzeli. "Review on the QM/MM Methodologies and Their Application to Metalloproteins." Molecules 27, no. 9 (April 20, 2022): 2660. http://dx.doi.org/10.3390/molecules27092660.
Повний текст джерелаKhrenova, Maria G., Egor S. Bulavko, Fedor D. Mulashkin, and Alexander V. Nemukhin. "Mechanism of Guanosine Triphosphate Hydrolysis by the Visual Proteins Arl3-RP2: Free Energy Reaction Profiles Computed with Ab Initio Type QM/MM Potentials." Molecules 26, no. 13 (June 30, 2021): 3998. http://dx.doi.org/10.3390/molecules26133998.
Повний текст джерелаArdevol, Albert, and Gerhard Hummer. "Retinal isomerization and water-pore formation in channelrhodopsin-2." Proceedings of the National Academy of Sciences 115, no. 14 (March 19, 2018): 3557–62. http://dx.doi.org/10.1073/pnas.1700091115.
Повний текст джерелаWatanabe, Hiroshi. "Improvement of Performance, Stability and Continuity by Modified Size-Consistent Multipartitioning Quantum Mechanical/Molecular Mechanical Method." Molecules 23, no. 8 (July 27, 2018): 1882. http://dx.doi.org/10.3390/molecules23081882.
Повний текст джерелаPeguiron, Anke, Lucio Colombi Ciacchi, Alessandro De Vita, James R. Kermode, and Gianpietro Moras. "Accuracy of buffered-force QM/MM simulations of silica." Journal of Chemical Physics 142, no. 6 (February 14, 2015): 064116. http://dx.doi.org/10.1063/1.4907786.
Повний текст джерелаMessner, Christoph B., Günther K. Bonn, and Thomas S. Hofer. "QM/MM MD simulations of La(iii)–phosphopeptide complexes." Molecular BioSystems 11, no. 1 (2015): 232–38. http://dx.doi.org/10.1039/c4mb00424h.
Повний текст джерелаWang, Meiting, Ye Mei, and Ulf Ryde. "Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations." Journal of Chemical Theory and Computation 14, no. 12 (October 26, 2018): 6613–22. http://dx.doi.org/10.1021/acs.jctc.8b00685.
Повний текст джерелаBulo, Rosa E., Bernd Ensing, Jetze Sikkema, and Lucas Visscher. "Toward a Practical Method for Adaptive QM/MM Simulations." Journal of Chemical Theory and Computation 5, no. 9 (July 30, 2009): 2212–21. http://dx.doi.org/10.1021/ct900148e.
Повний текст джерелаLu, Xiya, Dong Fang, Shingo Ito, Yuko Okamoto, Victor Ovchinnikov, and Qiang Cui. "QM/MM free energy simulations: recent progress and challenges." Molecular Simulation 42, no. 13 (July 5, 2016): 1056–78. http://dx.doi.org/10.1080/08927022.2015.1132317.
Повний текст джерелаCooper, April M., and Johannes Kästner. "Averaging Techniques for Reaction Barriers in QM/MM Simulations." ChemPhysChem 15, no. 15 (September 5, 2014): 3264–69. http://dx.doi.org/10.1002/cphc.201402382.
Повний текст джерелаSun, Zhaoxi. "BAR-based multi-dimensional nonequilibrium pulling for indirect construction of QM/MM free energy landscapes: from semi-empirical to ab initio." Physical Chemistry Chemical Physics 21, no. 39 (2019): 21942–59. http://dx.doi.org/10.1039/c9cp04113c.
Повний текст джерелаLev, Bogdan, Benoît Roux, and Sergei Yu Noskov. "Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations." Journal of Chemical Theory and Computation 9, no. 9 (August 26, 2013): 4165–75. http://dx.doi.org/10.1021/ct400296w.
Повний текст джерелаPratihar, Subha, George L. Barnes, and William L. Hase. "Chemical dynamics simulations of energy transfer, surface-induced dissociation, soft-landing, and reactive-landing in collisions of protonated peptide ions with organic surfaces." Chemical Society Reviews 45, no. 13 (2016): 3595–608. http://dx.doi.org/10.1039/c5cs00482a.
Повний текст джерелаSenn, Hans Martin, Johannes Kästner, Jürgen Breidung, and Walter Thiel. "Finite-temperature effects in enzymatic reactions — Insights from QM/MM free-energy simulations." Canadian Journal of Chemistry 87, no. 10 (October 2009): 1322–37. http://dx.doi.org/10.1139/v09-092.
Повний текст джерелаHofer, Thomas S., Andreas B. Pribil, and Bernhard R. Randolf. "Capabilities of chemical simulation methods in the elucidation of structure and dynamics of solutions." Pure and Applied Chemistry 80, no. 6 (January 1, 2008): 1195–210. http://dx.doi.org/10.1351/pac200880061195.
Повний текст джерелаDuster, Adam, Chun-Hung Wang, and Hai Lin. "Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes." Molecules 23, no. 9 (August 28, 2018): 2170. http://dx.doi.org/10.3390/molecules23092170.
Повний текст джерелаHofer, Thomas S. "Perspectives for hybrid ab initio/molecular mechanical simulations of solutions: from complex chemistry to proton-transfer reactions and interfaces." Pure and Applied Chemistry 86, no. 2 (February 1, 2014): 105–17. http://dx.doi.org/10.1515/pac-2014-5019.
Повний текст джерелаRiccardi, Demian, Patricia Schaefer, and Qiang Cui. "pKaCalculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations: A Quantitative Test of QM/MM Protocols." Journal of Physical Chemistry B 109, no. 37 (September 2005): 17715–33. http://dx.doi.org/10.1021/jp0517192.
Повний текст джерелаWymore, Troy, David W. Deerfield, Martin J. Field, John Hempel, and Hugh B. Nicholas. "Initial catalytic events in class 3 aldehyde dehydrogenase: MM and QM/MM simulations." Chemico-Biological Interactions 143-144 (February 2003): 75–84. http://dx.doi.org/10.1016/s0009-2797(02)00175-8.
Повний текст джерелаZurek, Jolanta, Anna L. Bowman, W. Andrzej Sokalski, and Adrian J. Mulholland. "MM and QM/MM Modeling of Threonyl-tRNA Synthetase: Model Testing and Simulations." Structural Chemistry 15, no. 5 (October 2004): 405–14. http://dx.doi.org/10.1023/b:stuc.0000037896.80027.2c.
Повний текст джерелаSchwenk, C. F., and B. M. Rode. "Ab initio QM/MM MD simulations of the hydrated Ca2+ ion." Pure and Applied Chemistry 76, no. 1 (January 1, 2004): 37–47. http://dx.doi.org/10.1351/pac200476010037.
Повний текст джерелаSaito, Toru, and Yu Takano. "QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease." Journal of Physical Chemistry B 126, no. 10 (March 3, 2022): 2087–97. http://dx.doi.org/10.1021/acs.jpcb.1c10200.
Повний текст джерелаCurchod, Basile F. E., Pabloc Campomanes, Andrey Laktionov, Marilisa Neri, Thomas J. Penfold, Stefano Vanni, Ivano Tavernelli, and Ursula Rothlisberger. "Mechanical (QM/MM) Simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena." CHIMIA International Journal for Chemistry 65, no. 5 (May 26, 2011): 330–33. http://dx.doi.org/10.2533/chimia.2011.330.
Повний текст джерелаAcevedo, Orlando, and William L. Jorgensen. "Cope Elimination: Elucidation of Solvent Effects from QM/MM Simulations." Journal of the American Chemical Society 128, no. 18 (May 2006): 6141–46. http://dx.doi.org/10.1021/ja057523x.
Повний текст джерелаRiccardi, Demian, Guohui Li, and Qiang Cui. "Importance of van der Waals Interactions in QM/MM Simulations." Journal of Physical Chemistry B 108, no. 20 (May 2004): 6467–78. http://dx.doi.org/10.1021/jp037992q.
Повний текст джерелаHudson, Phillip S., H. Lee Woodcock, and Stefan Boresch. "Use of Interaction Energies in QM/MM Free Energy Simulations." Journal of Chemical Theory and Computation 15, no. 8 (May 29, 2019): 4632–45. http://dx.doi.org/10.1021/acs.jctc.9b00084.
Повний текст джерелаGovender, Krishna K., and Kevin J. Naidoo. "Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations." Journal of Chemical Theory and Computation 10, no. 10 (September 18, 2014): 4708–17. http://dx.doi.org/10.1021/ct500373p.
Повний текст джерелаLambros, Eleftherios, Filippo Lipparini, Gerardo Andrés Cisneros, and Francesco Paesani. "A Many-Body, Fully Polarizable Approach to QM/MM Simulations." Journal of Chemical Theory and Computation 16, no. 12 (November 19, 2020): 7462–72. http://dx.doi.org/10.1021/acs.jctc.0c00932.
Повний текст джерелаDifley, Seth, Lee-Ping Wang, Sina Yeganeh, Shane R. Yost, and Troy Van Voorhis. "Electronic Properties of Disordered Organic Semiconductors via QM/MM Simulations." Accounts of Chemical Research 43, no. 7 (July 20, 2010): 995–1004. http://dx.doi.org/10.1021/ar900246s.
Повний текст джерелаHORI, TAKUMI, HIDEAKI TAKAHASHI, and TOMOSHIGE NITTA. "HYBRID QUANTUM MECHANICAL/MOLECULAR MECHANICAL APPROACH TO ENZYMATIC REACTIONS BY UTILIZING THE REAL-SPACE GRID TECHNIQUE." Journal of Theoretical and Computational Chemistry 04, no. 03 (September 2005): 867–82. http://dx.doi.org/10.1142/s0219633605001799.
Повний текст джерелаKulik, Heather J. "Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer." Physical Chemistry Chemical Physics 20, no. 31 (2018): 20650–60. http://dx.doi.org/10.1039/c8cp03871f.
Повний текст джерелаHui, Chenggong, Warispreet Singh, Derek Quinn, Chun Li, Thomas S. Moody, and Meilan Huang. "Regio- and stereoselectivity in the CYP450BM3-catalyzed hydroxylation of complex terpenoids: a QM/MM study." Physical Chemistry Chemical Physics 22, no. 38 (2020): 21696–706. http://dx.doi.org/10.1039/d0cp03083j.
Повний текст джерелаSzabla, Rafał, Holger Kruse, Petr Stadlbauer, Jiří Šponer, and Andrzej L. Sobolewski. "Sequential electron transfer governs the UV-induced self-repair of DNA photolesions." Chemical Science 9, no. 12 (2018): 3131–40. http://dx.doi.org/10.1039/c8sc00024g.
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