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For: Pan X, Nam K, Epifanovsky E, Simmonett AC, Rosta E, Shao Y. A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations. J Chem Phys 2021;154:024115. [PMID: 33445891 DOI: 10.1063/5.0038120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
Number Cited by Other Article(s)
1
Van R, Pan X, Rostami S, Liu J, Agarwal PK, Brooks B, Rajan R, Shao Y. Exploring CRISPR-Cas9 HNH-Domain-Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation. Biochemistry 2024. [PMID: 39680038 DOI: 10.1021/acs.biochem.4c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
2
Bonfrate S, Ferré N, Huix-Rotllant M. Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators. J Chem Theory Comput 2024;20:4338-4349. [PMID: 38712506 DOI: 10.1021/acs.jctc.4c00201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
3
Pan X, Snyder R, Wang JN, Lander C, Wickizer C, Van R, Chesney A, Xue Y, Mao Y, Mei Y, Pu J, Shao Y. Training machine learning potentials for reactive systems: A Colab tutorial on basic models. J Comput Chem 2024;45:638-647. [PMID: 38082539 PMCID: PMC10923003 DOI: 10.1002/jcc.27269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 01/18/2024]
4
Pan X, Van R, Pu J, Nam K, Mao Y, Shao Y. Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions. J Chem Theory Comput 2023;19:8234-8244. [PMID: 37943896 PMCID: PMC10835707 DOI: 10.1021/acs.jctc.3c00973] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
5
Abbas SJ, Yesmin S, Xia F, Ali SI, Xiao Z, Tan W. Oligonucleotide nanoassemblies with allyl bromide scaffold-based small molecules. DISCOVER NANO 2023;18:81. [PMID: 37382753 DOI: 10.1186/s11671-023-03846-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/05/2023] [Indexed: 06/30/2023]
6
Csizi K, Reiher M. Universal QM / MM approaches for general nanoscale applications. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
7
Yao S, Van R, Pan X, Park JH, Mao Y, Pu J, Mei Y, Shao Y. Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations. RSC Adv 2023;13:4565-4577. [PMID: 36760282 PMCID: PMC9900604 DOI: 10.1039/d2ra08180f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023]  Open
8
Kar RK. Benefits of hybrid QM/MM over traditional classical mechanics in pharmaceutical systems. Drug Discov Today 2023;28:103374. [PMID: 36174967 DOI: 10.1016/j.drudis.2022.103374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/27/2022] [Accepted: 09/22/2022] [Indexed: 02/02/2023]
9
Giese TJ, Zeng J, Ekesan Ş, York DM. Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions. J Chem Theory Comput 2022;18:4304-4317. [PMID: 35709391 PMCID: PMC9283286 DOI: 10.1021/acs.jctc.2c00151] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
10
Pan X, Van R, Epifanovsky E, Liu J, Pu J, Nam K, Shao Y. Accelerating Ab Initio Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian. J Phys Chem B 2022;126:10.1021/acs.jpcb.2c02262. [PMID: 35653199 PMCID: PMC9715852 DOI: 10.1021/acs.jpcb.2c02262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
11
Neves RPP, Cunha AV, Fernandes PA, Ramos MJ. Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms. Chemphyschem 2022;23:e202200159. [PMID: 35499146 DOI: 10.1002/cphc.202200159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/28/2022] [Indexed: 11/07/2022]
12
Pederson JP, McDaniel J. DFT-based QM/MM with Particle-Mesh Ewald for Direct, Long-Range Electrostatic Embedding. J Chem Phys 2022;156:174105. [DOI: 10.1063/5.0087386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
13
Gómez-Flores CL, Maag D, Kansari M, Vuong VQ, Irle S, Gräter F, Kubař T, Elstner M. Accurate Free Energies for Complex Condensed-Phase Reactions Using an Artificial Neural Network Corrected DFTB/MM Methodology. J Chem Theory Comput 2022;18:1213-1226. [PMID: 34978438 DOI: 10.1021/acs.jctc.1c00811] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
14
Le Breton G, Bonhomme O, Benichou E, Loison C. First Hyperpolarizability of Water in Bulk Liquid Phase: Long-Range Electrostatic Effects Included via the Second Hyperpolarizability. Phys Chem Chem Phys 2022;24:19463-19472. [DOI: 10.1039/d2cp00803c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
15
Reinholdt P, Kongsted J, Lipparini F. Fast Approximate but Accurate QM/MM Interactions for Polarizable Embedding. J Chem Theory Comput 2021;18:344-356. [PMID: 34951300 DOI: 10.1021/acs.jctc.1c01037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
16
Kirsch T, Olsen JMH, Bolnykh V, Meloni S, Ippoliti E, Rothlisberger U, Cascella M, Gauss J. Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC. J Chem Theory Comput 2021;18:13-24. [PMID: 34905353 DOI: 10.1021/acs.jctc.1c00878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
17
Pan X, Yang J, Van R, Epifanovsky E, Ho J, Huang J, Pu J, Mei Y, Nam K, Shao Y. Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions. J Chem Theory Comput 2021;17:5745-5758. [PMID: 34468138 PMCID: PMC9070000 DOI: 10.1021/acs.jctc.1c00565] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
18
Cruzeiro VWD, Manathunga M, Merz KM, Götz AW. Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK. J Chem Inf Model 2021;61:2109-2115. [PMID: 33913331 DOI: 10.1021/acs.jcim.1c00169] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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