• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4608411)   Today's Articles (4842)   Subscriber (49375)
For: Bui JM, Henchman RH, McCammon JA. The dynamics of ligand barrier crossing inside the acetylcholinesterase gorge. Biophys J 2004;85:2267-72. [PMID: 14507691 PMCID: PMC1303452 DOI: 10.1016/s0006-3495(03)74651-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
Number Cited by Other Article(s)
1
Richmond V, Falcone BN, Maier MS, Arroyo Máñez P. Putting the Puzzle Together To Get the Whole Picture: Molecular Basis of the Affinity of Two Steroid Derivatives to Acetylcholinesterase. ACS OMEGA 2023;8:25610-25622. [PMID: 37483177 PMCID: PMC10357547 DOI: 10.1021/acsomega.3c03749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 07/25/2023]
2
Bagri K, Kumar A, Manisha, Kumar P. Computational Studies on Acetylcholinesterase Inhibitors: From Biochemistry to Chemistry. Mini Rev Med Chem 2021;20:1403-1435. [PMID: 31884928 DOI: 10.2174/1389557520666191224144346] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 11/22/2022]
3
Limongelli V. Ligand binding free energy and kinetics calculation in 2020. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1455] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
4
Bernetti M, Masetti M, Rocchia W, Cavalli A. Kinetics of Drug Binding and Residence Time. Annu Rev Phys Chem 2019;70:143-171. [DOI: 10.1146/annurev-physchem-042018-052340] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
5
Deganutti G, Zhukov A, Deflorian F, Federico S, Spalluto G, Cooke RM, Moro S, Mason JS, Bortolato A. Impact of protein-ligand solvation and desolvation on transition state thermodynamic properties of adenosine A2A ligand binding kinetics. In Silico Pharmacol 2017;5:16. [PMID: 29308352 PMCID: PMC5755719 DOI: 10.1007/s40203-017-0037-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/14/2017] [Indexed: 12/26/2022]  Open
6
Xu Y, Cheng S, Sussman JL, Silman I, Jiang H. Computational Studies on Acetylcholinesterases. Molecules 2017;22:molecules22081324. [PMID: 28796192 PMCID: PMC6152020 DOI: 10.3390/molecules22081324] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/07/2017] [Accepted: 08/07/2017] [Indexed: 01/18/2023]  Open
7
Ismaili L, Refouvelet B, Benchekroun M, Brogi S, Brindisi M, Gemma S, Campiani G, Filipic S, Agbaba D, Esteban G, Unzeta M, Nikolic K, Butini S, Marco-Contelles J. Multitarget compounds bearing tacrine- and donepezil-like structural and functional motifs for the potential treatment of Alzheimer's disease. Prog Neurobiol 2017;151:4-34. [DOI: 10.1016/j.pneurobio.2015.12.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 11/11/2015] [Accepted: 12/11/2015] [Indexed: 01/16/2023]
8
Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies. Future Med Chem 2017;9:507-523. [DOI: 10.4155/fmc-2016-0224] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
9
Okimoto N, Suenaga A, Taiji M. Evaluation of protein-ligand affinity prediction using steered molecular dynamics simulations. J Biomol Struct Dyn 2016;35:3221-3231. [PMID: 27771988 DOI: 10.1080/07391102.2016.1251851] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
10
De Vivo M, Masetti M, Bottegoni G, Cavalli A. Role of Molecular Dynamics and Related Methods in Drug Discovery. J Med Chem 2016;59:4035-61. [DOI: 10.1021/acs.jmedchem.5b01684] [Citation(s) in RCA: 538] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
11
Reilly PJ, Rovira C. Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
12
Bennion BJ, Essiz SG, Lau EY, Fattebert JL, Emigh A, Lightstone FC. A wrench in the works of human acetylcholinesterase: soman induced conformational changes revealed by molecular dynamics simulations. PLoS One 2015;10:e0121092. [PMID: 25874456 PMCID: PMC4395452 DOI: 10.1371/journal.pone.0121092] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/27/2015] [Indexed: 01/06/2023]  Open
13
Cavalli A, Spitaleri A, Saladino G, Gervasio FL. Investigating drug-target association and dissociation mechanisms using metadynamics-based algorithms. Acc Chem Res 2015;48:277-85. [PMID: 25496113 DOI: 10.1021/ar500356n] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
14
Pathak AK, Bandyopadhyay T. Unbinding free energy of acetylcholinesterase bound oxime drugs along the gorge pathway from metadynamics-umbrella sampling investigation. Proteins 2014;82:1799-818. [PMID: 24549829 DOI: 10.1002/prot.24533] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/17/2014] [Accepted: 01/28/2014] [Indexed: 12/20/2022]
15
Gora A, Brezovsky J, Damborsky J. Gates of enzymes. Chem Rev 2013;113:5871-923. [PMID: 23617803 PMCID: PMC3744840 DOI: 10.1021/cr300384w] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Indexed: 12/15/2022]
16
Mutunga JM, Boina DR, Anderson TD, Bloomquist JR, Carlier PR, Wong DM, Lam PCH, Totrov MM. Neurotoxicology of bis(n)-tacrines on Blattella germanica and Drosophila melanogaster acetylcholinesterase. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2013;83:180-194. [PMID: 23740645 PMCID: PMC4739519 DOI: 10.1002/arch.21104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
17
Sinha V, Ganguly B, Bandyopadhyay T. Energetics of Ortho-7 (oxime drug) translocation through the active-site gorge of tabun conjugated acetylcholinesterase. PLoS One 2012;7:e40188. [PMID: 22808117 PMCID: PMC3394793 DOI: 10.1371/journal.pone.0040188] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 06/02/2012] [Indexed: 11/19/2022]  Open
18
Saladino G, Gauthier L, Bianciotto M, Gervasio FL. Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors. J Chem Theory Comput 2012;8:1165-70. [DOI: 10.1021/ct3001377] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
19
Lee S, Kim JH, Lee S. Internal Diffusion-Controlled Enzyme Reaction: The Acetylcholinesterase Kinetics. J Chem Theory Comput 2012;8:715-23. [PMID: 26596618 DOI: 10.1021/ct2006727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
20
Kalyaanamoorthy S, Chen YPP. Exploring inhibitor release pathways in histone deacetylases using random acceleration molecular dynamics simulations. J Chem Inf Model 2012;52:589-603. [PMID: 22263580 DOI: 10.1021/ci200584f] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
21
Patel JS, Branduardi D, Masetti M, Rocchia W, Cavalli A. Insights into Ligand-Protein Binding from Local Mechanical Response. J Chem Theory Comput 2011;7:3368-3378. [PMID: 22003321 PMCID: PMC3191767 DOI: 10.1021/ct200324j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Indexed: 11/28/2022]
22
McCammon JA. Gated Diffusion-controlled Reactions. BMC BIOPHYSICS 2011;4:4. [PMID: 21595999 PMCID: PMC3093672 DOI: 10.1186/2046-1682-4-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 03/02/2011] [Indexed: 11/28/2022]
23
Fidelak J, Juraszek J, Branduardi D, Bianciotto M, Gervasio FL. Free-energy-based methods for binding profile determination in a congeneric series of CDK2 inhibitors. J Phys Chem B 2010;114:9516-24. [PMID: 20593892 DOI: 10.1021/jp911689r] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
24
Correlation between the substrate structure and the rate of acetylcholinesterase hydrolysis modeled with the combined quantum mechanical/molecular mechanical studies. Chem Biol Interact 2010;187:59-63. [DOI: 10.1016/j.cbi.2010.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 03/26/2010] [Accepted: 04/06/2010] [Indexed: 11/22/2022]
25
Knott BC, Duff N, Doherty MF, Peters B. Estimating diffusivity along a reaction coordinate in the high friction limit: Insights on pulse times in laser-induced nucleation. J Chem Phys 2009;131:224112. [DOI: 10.1063/1.3268704] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
26
Klvana M, Pavlova M, Koudelakova T, Chaloupkova R, Dvorak P, Prokop Z, Stsiapanava A, Kuty M, Kuta-Smatanova I, Dohnalek J, Kulhanek P, Wade RC, Damborsky J. Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations. J Mol Biol 2009;392:1339-56. [PMID: 19577578 DOI: 10.1016/j.jmb.2009.06.076] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 06/25/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
27
Doudou S, Burton NA, Henchman RH. Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force. J Chem Theory Comput 2009;5:909-18. [PMID: 26609600 DOI: 10.1021/ct8002354] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
28
Vallverdu G, Demachy I, Ridard J, Lévy B. Using biased molecular dynamics and Brownian dynamics in the study of fluorescent proteins. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.07.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
29
Bui JM, Andrew McCammon J. Intrinsic conformational flexibility of acetylcholinesterase. Chem Biol Interact 2008;175:303-4. [PMID: 18452905 DOI: 10.1016/j.cbi.2008.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2007] [Accepted: 03/04/2008] [Indexed: 11/17/2022]
30
Silman I, Sussman JL. Acetylcholinesterase: how is structure related to function? Chem Biol Interact 2008;175:3-10. [PMID: 18586019 DOI: 10.1016/j.cbi.2008.05.035] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2007] [Revised: 05/23/2008] [Accepted: 05/29/2008] [Indexed: 10/22/2022]
31
Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling. J Mol Model 2008;14:409-16. [DOI: 10.1007/s00894-008-0287-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Accepted: 02/08/2008] [Indexed: 10/22/2022]
32
Petraglio G, Bartolini M, Branduardi D, Andrisano V, Recanatini M, Gervasio FL, Cavalli A, Parrinello M. The role of Li + , Na + , and K + in the ligand binding inside the human acetylcholinesterase gorge. Proteins 2008;70:779-85. [PMID: 17729290 DOI: 10.1002/prot.21560] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
33
Structural features of neutral and protonated galanthamine: A crystallographic database and computational investigation. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2006.07.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
34
Molecular dynamics simulations of human butyrylcholinesterase. Proteins 2006;59:104-17. [PMID: 15696543 DOI: 10.1002/prot.20398] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
PrevPage 1 of 1 1Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA