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Number Cited by Other Article(s)
1
Liu P, Li Y, Liu Y, Liu J, Dong K, Jia Q. Molecular Insights into the Binding Behavior of Imidazolium Ionic Liquids to the Receptor Binding Domain of the SARS-CoV-2 Spike Protein. J Phys Chem B 2023;127:4396-4405. [PMID: 37194950 DOI: 10.1021/acs.jpcb.3c00593] [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: 05/18/2023]
2
Wang Q, Liu S, Li K, Xing R, Chen X, Li P. A Computational Biology Study on the Structure and Dynamics Determinants of Thermal Stability of the Chitosanase from Aspergillus fumigatus. Int J Mol Sci 2023;24:ijms24076671. [PMID: 37047643 PMCID: PMC10095384 DOI: 10.3390/ijms24076671] [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: 02/19/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023]  Open
3
Harada R, Morita R, Shigeta Y. Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods. J Chem Inf Model 2023;63:259-269. [PMID: 36574612 DOI: 10.1021/acs.jcim.2c01097] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
4
Boopathi S, Garduño‐Juárez R. Calcium inhibits penetration of Alzheimer's Aβ1 -42 monomers into the membrane. Proteins 2022;90:2124-2143. [PMID: 36321654 PMCID: PMC9804374 DOI: 10.1002/prot.26403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/08/2022] [Accepted: 07/25/2022] [Indexed: 01/05/2023]
5
Yang Y, Distaffen H, Jalali S, Nieuwkoop AJ, Nilsson BL, Dias CL. Atomic Insights into Amyloid-Induced Membrane Damage. ACS Chem Neurosci 2022;13:2766-2777. [PMID: 36095304 DOI: 10.1021/acschemneuro.2c00446] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]  Open
6
Press-Sandler O, Miller Y. Molecular insights into the primary nucleation of polymorphic amyloid β dimers in DOPC lipid bilayer membrane. Protein Sci 2022;31:e4283. [PMID: 35129859 PMCID: PMC8994488 DOI: 10.1002/pro.4283] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/29/2022]
7
Boopathi S, Poma AB, Garduño-Juárez R. An Overview of Several Inhibitors for Alzheimer's Disease: Characterization and Failure. Int J Mol Sci 2021;22:10798. [PMID: 34639140 PMCID: PMC8509255 DOI: 10.3390/ijms221910798] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 01/04/2023]  Open
8
Tran TT, Pan F, Tran L, Roland C, Sagui C. The F19W mutation reduces the binding affinity of the transmembrane Aβ11-40 trimer to the membrane bilayer. RSC Adv 2021;11:2664-2676. [PMID: 35424222 PMCID: PMC8693879 DOI: 10.1039/d0ra08837d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022]  Open
9
Assessing the role of osmolytes on the conformational harmony of islet amyloid polypeptide. Int J Biol Macromol 2020;164:2569-2582. [DOI: 10.1016/j.ijbiomac.2020.08.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
10
Ganesan M, Paranthaman S. Studies on the structure and conformational flexibility of secondary structures in amyloid beta — A quantum chemical study. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020. [DOI: 10.1142/s0219633620500145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
11
Highlighting the effect of amyloid beta assemblies on the mechanical properties and conformational stability of cell membrane. J Mol Graph Model 2020;100:107670. [PMID: 32711259 DOI: 10.1016/j.jmgm.2020.107670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 01/05/2023]
12
Saravanan KM, Zhang H, Zhang H, Xi W, Wei Y. On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective. Front Bioeng Biotechnol 2020;8:532. [PMID: 32656188 PMCID: PMC7325929 DOI: 10.3389/fbioe.2020.00532] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/04/2020] [Indexed: 12/12/2022]  Open
13
Ngo ST, Nguyen PH, Derreumaux P. Stability of Aβ11-40 Trimers with Parallel and Antiparallel β-Sheet Organizations in a Membrane-Mimicking Environment by Replica Exchange Molecular Dynamics Simulation. J Phys Chem B 2020;124:617-626. [PMID: 31931566 DOI: 10.1021/acs.jpcb.9b10982] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
14
Kumari A, Somvanshi P, Grover A. Ameliorating amyloid aggregation through osmolytes as a probable therapeutic molecule against Alzheimer's disease and type 2 diabetes. RSC Adv 2020;10:12166-12182. [PMID: 35497581 PMCID: PMC9050657 DOI: 10.1039/d0ra00429d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/16/2020] [Indexed: 01/31/2023]  Open
15
Ngo ST, Nguyen TH, Tung NT, Nam PC, Vu KB, Vu VV. Oversampling Free Energy Perturbation Simulation in Determination of the Ligand‐Binding Free Energy. J Comput Chem 2019;41:611-618. [DOI: 10.1002/jcc.26130] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/01/2019] [Accepted: 12/02/2019] [Indexed: 12/14/2022]
16
Prediction of AChE-ligand affinity using the umbrella sampling simulation. J Mol Graph Model 2019;93:107441. [DOI: 10.1016/j.jmgm.2019.107441] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 08/02/2019] [Accepted: 08/26/2019] [Indexed: 11/18/2022]
17
Tung N, Derreumaux P, Vu VV, Nam PC, Ngo ST. C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ11-42 Tetramer in Solution: Intensive MD Study. ACS OMEGA 2019;4:11066-11073. [PMID: 31460204 PMCID: PMC6648102 DOI: 10.1021/acsomega.9b00992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/27/2019] [Indexed: 06/10/2023]
18
Venable RM, Krämer A, Pastor RW. Molecular Dynamics Simulations of Membrane Permeability. Chem Rev 2019;119:5954-5997. [PMID: 30747524 PMCID: PMC6506413 DOI: 10.1021/acs.chemrev.8b00486] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
19
Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019;119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
20
Ngo ST, Derreumaux P, Vu VV. Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca2+ Ions. J Phys Chem B 2019;123:2645-2653. [DOI: 10.1021/acs.jpcb.8b10792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
21
Sahoo A, Matysiak S. Computational insights into lipid assisted peptide misfolding and aggregation in neurodegeneration. Phys Chem Chem Phys 2019;21:22679-22694. [DOI: 10.1039/c9cp02765c] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
22
Etersalate prevents the formations of 6Aβ16-22 oligomer: An in silico study. PLoS One 2018;13:e0204026. [PMID: 30226897 PMCID: PMC6143259 DOI: 10.1371/journal.pone.0204026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 09/01/2018] [Indexed: 11/19/2022]  Open
23
Press-Sandler O, Miller Y. Molecular mechanisms of membrane-associated amyloid aggregation: Computational perspective and challenges. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018;1860:1889-1905. [DOI: 10.1016/j.bbamem.2018.03.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 01/02/2023]
24
Ngo ST, Hung HM, Hong ND, Tung NT. The influences of E22Q mutant on solvated 3Aβ11-40 peptide: A REMD study. J Mol Graph Model 2018;83:122-128. [PMID: 29902674 DOI: 10.1016/j.jmgm.2018.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/03/2018] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
25
Computational Insight into the Effect of Natural Compounds on the Destabilization of Preformed Amyloid-β(1⁻40) Fibrils. Molecules 2018;23:molecules23061320. [PMID: 29857500 PMCID: PMC6100107 DOI: 10.3390/molecules23061320] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/31/2022]  Open
26
Propafenone effects on the stable structures of Aβ16-22 system. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.02.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
27
Amyloid growth and membrane damage: Current themes and emerging perspectives from theory and experiments on Aβ and hIAPP. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018;1860:1625-1638. [PMID: 29501606 DOI: 10.1016/j.bbamem.2018.02.022] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/21/2018] [Accepted: 02/21/2018] [Indexed: 12/15/2022]
28
Ngo ST, Thu Phung HT, Vu KB, Vu VV. Atomistic investigation of an Iowa Amyloid-β trimer in aqueous solution. RSC Adv 2018;8:41705-41712. [PMID: 35558787 PMCID: PMC9091969 DOI: 10.1039/c8ra07615d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/04/2018] [Indexed: 11/21/2022]  Open
29
Ngo ST, Nguyen MT, Nguyen NT, Vu VV. The Effects of A21G Mutation on Transmembrane Amyloid Beta (11–40) Trimer: An In Silico Study. J Phys Chem B 2017;121:8467-8474. [DOI: 10.1021/acs.jpcb.7b05906] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
30
Evaluation of the absolute affinity of neuraminidase inhibitor using steered molecular dynamics simulations. J Mol Graph Model 2017;77:137-142. [PMID: 28854402 DOI: 10.1016/j.jmgm.2017.08.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 11/20/2022]
31
EGCG inhibits the oligomerization of amyloid beta (16-22) hexamer: Theoretical studies. J Mol Graph Model 2017;76:1-10. [PMID: 28658644 DOI: 10.1016/j.jmgm.2017.06.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 11/21/2022]
32
Ngo ST, Nguyen MT, Nguyen MT. Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
33
Ngo ST, Luu XC, Nguyen MT, Le CN, Vu VV. In silico studies of solvated F19W amyloid β (11–40) trimer. RSC Adv 2017. [DOI: 10.1039/c7ra07187f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
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