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For: Meuwly M. Reactive molecular dynamics: From small molecules to proteins. WIREs Comput Mol Sci 2018. [DOI: 10.1002/wcms.1386] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Number Cited by Other Article(s)
1
Yang J, Guo H, Liu S, Xi K, Wu Q, Li Y, Fang K, Zhou K, Su C, Jing BY, Wu H, Zhu L. Locating Transition States for Biomolecular Dynamics via Invertible Dimensionality Reduction. J Chem Theory Comput 2025. [PMID: 40390308 DOI: 10.1021/acs.jctc.4c01624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2025]
2
Yang Y, Zhang S, Ranasinghe KD, Isayev O, Roitberg AE. Machine Learning of Reactive Potentials. Annu Rev Phys Chem 2024;75:371-395. [PMID: 38941524 DOI: 10.1146/annurev-physchem-062123-024417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
3
Chen W, Zhang Y, Qiang Q, Zou L, Zou P, Xu Y. Pinobanksin from peony seed husk: A flavonoid with the potential to inhibit the proliferation of SH-SY5Y. Food Sci Nutr 2024;12:815-829. [PMID: 38370064 PMCID: PMC10867468 DOI: 10.1002/fsn3.3786] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/14/2023] [Accepted: 10/08/2023] [Indexed: 02/20/2024]  Open
4
Jacobsen L, Lydersen L, Khandelia H. ATP-Bound State of the Uncoupling Protein 1 (UCP1) from Molecular Simulations. J Phys Chem B 2023;127:9685-9696. [PMID: 37921649 DOI: 10.1021/acs.jpcb.3c03473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
5
Zhang L, Yao L, Zhao F, Yu A, Zhou Y, Wen Q, Wang J, Zheng T, Chen P. Protein and Peptide-Based Nanotechnology for Enhancing Stability, Bioactivity, and Delivery of Anthocyanins. Adv Healthc Mater 2023;12:e2300473. [PMID: 37537383 PMCID: PMC11468125 DOI: 10.1002/adhm.202300473] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/18/2023] [Indexed: 08/05/2023]
6
Xing C, Chen P, Zhang L. Computational insight into stability-enhanced systems of anthocyanin with protein/peptide. FOOD CHEMISTRY. MOLECULAR SCIENCES 2023;6:100168. [PMID: 36923156 PMCID: PMC10009195 DOI: 10.1016/j.fochms.2023.100168] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/24/2022] [Accepted: 02/18/2023] [Indexed: 02/24/2023]
7
Alizadeh Sahraei A, Azizi D, Mokarizadeh AH, Boffito DC, Larachi F. Emerging Trends of Computational Chemistry and Molecular Modeling in Froth Flotation: A Review. ACS ENGINEERING AU 2023;3:128-164. [PMID: 37362006 PMCID: PMC10288516 DOI: 10.1021/acsengineeringau.2c00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 06/28/2023]
8
Sami S, Marrink SJ. Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations. J Chem Theory Comput 2023. [PMID: 37327401 DOI: 10.1021/acs.jctc.2c01186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
9
Bosia F, Zheng P, Vaucher A, Weymuth T, Dral PO, Reiher M. Ultra-fast semi-empirical quantum chemistry for high-throughput computational campaigns with Sparrow. J Chem Phys 2023;158:054118. [PMID: 36754821 DOI: 10.1063/5.0136404] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
10
Alaghemandi M, Salehi L, Samolis P, Trachtenberg BT, Turnali A, Sander MY, Sharifzadeh S. Atomic understanding of structural deformations upon ablation of graphene. NANO SELECT 2021. [DOI: 10.1002/nano.202000248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
11
Pezeshkian W, Marrink SJ. Simulating realistic membrane shapes. Curr Opin Cell Biol 2021;71:103-111. [PMID: 33721706 DOI: 10.1016/j.ceb.2021.02.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 12/12/2022]
12
Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation. Nat Commun 2020;11:5713. [PMID: 33177517 PMCID: PMC7658983 DOI: 10.1038/s41467-020-19497-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022]  Open
13
Gissinger JR, Jensen BD, Wise KE. REACTER: A Heuristic Method for Reactive Molecular Dynamics. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c02012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
14
Rice BM, Mattson WD, Larentzos JP, Byrd EFC. Heuristics for chemical species identification in dense systems. J Chem Phys 2020;153:064102. [DOI: 10.1063/5.0015664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
15
Young JM, Mondal A, Barckholtz TA, Kiss G, Koziol L, Panagiotopoulos AZ. Predicting chemical reaction equilibria in molten carbonate fuel cells via molecular simulations. AIChE J 2020. [DOI: 10.1002/aic.16988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
16
Lindsey RK, Goldman N, Fried LE, Bastea S. Many-body reactive force field development for carbon condensation in C/O systems under extreme conditions. J Chem Phys 2020;153:054103. [DOI: 10.1063/5.0012840] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]  Open
17
Capelli R, Lyu W, Bolnykh V, Meloni S, Olsen JMH, Rothlisberger U, Parrinello M, Carloni P. Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study. J Phys Chem Lett 2020;11:6373-6381. [PMID: 32672983 DOI: 10.1021/acs.jpclett.0c00999] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
18
Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review. Catalysts 2020. [DOI: 10.3390/catal10060691] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
19
Käser S, Unke OT, Meuwly M. Isomerization and decomposition reactions of acetaldehyde relevant to atmospheric processes from dynamics simulations on neural network-based potential energy surfaces. J Chem Phys 2020;152:214304. [DOI: 10.1063/5.0008223] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
20
Multistate Reactive Molecular Dynamics Simulations of Proton Diffusion in Water Clusters and in the Bulk. J Phys Chem B 2019;123:9846-9861. [PMID: 31647873 DOI: 10.1021/acs.jpcb.9b03258] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
21
Rivero U, Unke OT, Meuwly M, Willitsch S. Reactive atomistic simulations of Diels-Alder reactions: The importance of molecular rotations. J Chem Phys 2019;151:104301. [DOI: 10.1063/1.5114981] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
22
Unke OT, Brickel S, Meuwly M. Sampling reactive regions in phase space by following the minimum dynamic path. J Chem Phys 2019;150:074107. [DOI: 10.1063/1.5082885] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]  Open
23
Simm GN, Vaucher AC, Reiher M. Exploration of Reaction Pathways and Chemical Transformation Networks. J Phys Chem A 2018;123:385-399. [DOI: 10.1021/acs.jpca.8b10007] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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