BPG is committed to discovery and dissemination of knowledge
Cited by in F6Publishing
For: Hénin J, Tajkhorshid E, Schulten K, Chipot C. Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophys J 2008;94:832-9. [PMID: 17921212 DOI: 10.1529/biophysj.107.115105] [Cited by in Crossref: 86] [Cited by in F6Publishing: 74] [Article Influence: 5.7] [Reference Citation Analysis]
Number Citing Articles
1 Hub JS, Grubmüller H, de Groot BL. Dynamics and Energetics of Permeation Through Aquaporins. What Do We Learn from Molecular Dynamics Simulations? In: Beitz E, editor. Aquaporins. Berlin: Springer Berlin Heidelberg; 2009. pp. 57-76. [DOI: 10.1007/978-3-540-79885-9_3] [Cited by in Crossref: 61] [Cited by in F6Publishing: 61] [Article Influence: 4.7] [Reference Citation Analysis]
2 Paul S, Paul TK, Taraphder S. Reaction Coordinate, Free Energy, and Rate of Intramolecular Proton Transfer in Human Carbonic Anhydrase II. J Phys Chem B 2018;122:2851-66. [DOI: 10.1021/acs.jpcb.7b10713] [Cited by in Crossref: 12] [Cited by in F6Publishing: 9] [Article Influence: 3.0] [Reference Citation Analysis]
3 Brändén M, Tabaei SR, Fischer G, Neutze R, Höök F. Refractive-index-based screening of membrane-protein-mediated transfer across biological membranes. Biophys J 2010;99:124-33. [PMID: 20655840 DOI: 10.1016/j.bpj.2010.03.059] [Cited by in Crossref: 30] [Cited by in F6Publishing: 27] [Article Influence: 2.5] [Reference Citation Analysis]
4 He X, Lopes PE, Mackerell AD Jr. Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator. Biopolymers 2013;99:724-38. [PMID: 23703219 DOI: 10.1002/bip.22286] [Cited by in Crossref: 44] [Cited by in F6Publishing: 33] [Article Influence: 7.3] [Reference Citation Analysis]
5 Tych K, Dougan L. A Single-Molecule Approach to Explore the Role of the Solvent Environment in Protein Folding. In: Ruso JM, Piñeiro Á, editors. Proteins in Solution and at Interfaces. Hoboken: John Wiley & Sons, Inc.; 2013. pp. 315-34. [DOI: 10.1002/9781118523063.ch15] [Cited by in Crossref: 2] [Article Influence: 0.2] [Reference Citation Analysis]
6 Bełdowski P, Kruszewska N, Yuvan S, Dendzik Z, Goudoulas T, Gadomski A. Capstan-like mechanism in hyaluronan-phospholipid systems. Chem Phys Lipids 2018;216:17-24. [PMID: 30144435 DOI: 10.1016/j.chemphyslip.2018.08.002] [Cited by in Crossref: 3] [Cited by in F6Publishing: 2] [Article Influence: 0.8] [Reference Citation Analysis]
7 Pan Y, Piyadasa H, O'Neil JD, Konermann L. Conformational dynamics of a membrane transport protein probed by H/D exchange and covalent labeling: the glycerol facilitator. J Mol Biol 2012;416:400-13. [PMID: 22227391 DOI: 10.1016/j.jmb.2011.12.052] [Cited by in Crossref: 42] [Cited by in F6Publishing: 38] [Article Influence: 3.8] [Reference Citation Analysis]
8 Garate J, English NJ, Macelroy JMD. Human aquaporin 4 gating dynamics in dc and ac electric fields: A molecular dynamics study. The Journal of Chemical Physics 2011;134:055110. [DOI: 10.1063/1.3529428] [Cited by in Crossref: 45] [Cited by in F6Publishing: 38] [Article Influence: 4.1] [Reference Citation Analysis]
9 Xu H, Cooke JE, Zwiazek JJ. Phylogenetic analysis of fungal aquaporins provides insight into their possible role in water transport of mycorrhizal associations. Botany 2013;91:495-504. [DOI: 10.1139/cjb-2013-0041] [Cited by in Crossref: 22] [Cited by in F6Publishing: 11] [Article Influence: 2.4] [Reference Citation Analysis]
10 Shiyun W, Enmin F. Stability of nonlinear microbial bioconversion system concerning glycerol’s active transport and 1,3-PD’s passive transport. Nonlinear Analysis: Real World Applications 2010;11:3501-11. [DOI: 10.1016/j.nonrwa.2009.12.011] [Cited by in Crossref: 9] [Article Influence: 0.8] [Reference Citation Analysis]
11 Ebert MCCJC, Guzman Espinola J, Lamoureux G, Pelletier JN. Substrate-Specific Screening for Mutational Hotspots Using Biased Molecular Dynamics Simulations. ACS Catal 2017;7:6786-97. [DOI: 10.1021/acscatal.7b02634] [Cited by in Crossref: 12] [Cited by in F6Publishing: 7] [Article Influence: 2.4] [Reference Citation Analysis]
12 Hu G, Yu X, Bian Y, Cao Z, Xu S, Zhao L, Ji B, Wang W, Wang J. Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism. Int J Mol Sci 2018;19:E3524. [PMID: 30423909 DOI: 10.3390/ijms19113524] [Cited by in Crossref: 7] [Cited by in F6Publishing: 7] [Article Influence: 1.8] [Reference Citation Analysis]
13 Moss FJ, Mahinthichaichan P, Lodowski DT, Kowatz T, Tajkhorshid E, Engel A, Boron WF, Vahedi-Faridi A. Aquaporin-7: A Dynamic Aquaglyceroporin With Greater Water and Glycerol Permeability Than Its Bacterial Homolog GlpF. Front Physiol 2020;11:728. [PMID: 32695023 DOI: 10.3389/fphys.2020.00728] [Cited by in Crossref: 8] [Cited by in F6Publishing: 5] [Article Influence: 4.0] [Reference Citation Analysis]
14 Chen LY. Glycerol modulates water permeation through Escherichia coli aquaglyceroporin GlpF. Biochim Biophys Acta 2013;1828:1786-93. [PMID: 23506682 DOI: 10.1016/j.bbamem.2013.03.008] [Cited by in Crossref: 22] [Cited by in F6Publishing: 23] [Article Influence: 2.4] [Reference Citation Analysis]
15 Dougan L, Genchev GZ, Lu H, Fernandez JM. Probing osmolyte participation in the unfolding transition state of a protein. Proc Natl Acad Sci U S A 2011;108:9759-64. [PMID: 21613570 DOI: 10.1073/pnas.1101934108] [Cited by in Crossref: 12] [Cited by in F6Publishing: 11] [Article Influence: 1.1] [Reference Citation Analysis]
16 Patel JS, Berteotti A, Ronsisvalle S, Rocchia W, Cavalli A. Steered molecular dynamics simulations for studying protein-ligand interaction in cyclin-dependent kinase 5. J Chem Inf Model 2014;54:470-80. [PMID: 24437446 DOI: 10.1021/ci4003574] [Cited by in Crossref: 96] [Cited by in F6Publishing: 83] [Article Influence: 12.0] [Reference Citation Analysis]
17 Enkavi G, Li J, Mahinthichaichan P, Wen PC, Huang Z, Shaikh SA, Tajkhorshid E. Simulation studies of the mechanism of membrane transporters. Methods Mol Biol 2013;924:361-405. [PMID: 23034756 DOI: 10.1007/978-1-62703-017-5_14] [Cited by in Crossref: 6] [Cited by in F6Publishing: 6] [Article Influence: 0.7] [Reference Citation Analysis]
18 Caballero J, Poblete H, Navarro C, Alzate-morales JH. Association of nicotinic acid with a poly(amidoamine) dendrimer studied by molecular dynamics simulations. Journal of Molecular Graphics and Modelling 2013;39:71-8. [DOI: 10.1016/j.jmgm.2012.11.003] [Cited by in Crossref: 22] [Cited by in F6Publishing: 18] [Article Influence: 2.4] [Reference Citation Analysis]
19 Pothier MP, Hinz AJ, Poulain AJ. Insights Into Arsenite and Arsenate Uptake Pathways Using a Whole Cell Biosensor. Front Microbiol 2018;9:2310. [PMID: 30333804 DOI: 10.3389/fmicb.2018.02310] [Cited by in Crossref: 7] [Cited by in F6Publishing: 3] [Article Influence: 1.8] [Reference Citation Analysis]
20 Mahinthichaichan P, Morris DM, Wang Y, Jensen GJ, Tajkhorshid E. Selective Permeability of Carboxysome Shell Pores to Anionic Molecules. J Phys Chem B 2018;122:9110-8. [PMID: 30193460 DOI: 10.1021/acs.jpcb.8b06822] [Cited by in Crossref: 25] [Cited by in F6Publishing: 18] [Article Influence: 6.3] [Reference Citation Analysis]
21 Hu G, Xu S, Wang J. Characterizing the Free-Energy Landscape of MDM2 Protein-Ligand Interactions by Steered Molecular Dynamics Simulations. Chem Biol Drug Des 2015;86:1351-9. [PMID: 26032728 DOI: 10.1111/cbdd.12598] [Cited by in Crossref: 17] [Cited by in F6Publishing: 16] [Article Influence: 2.4] [Reference Citation Analysis]
22 Gamini R, Sotomayor M, Chipot C, Schulten K. Cytoplasmic domain filter function in the mechanosensitive channel of small conductance. Biophys J 2011;101:80-9. [PMID: 21723817 DOI: 10.1016/j.bpj.2011.05.042] [Cited by in Crossref: 24] [Cited by in F6Publishing: 20] [Article Influence: 2.2] [Reference Citation Analysis]
23 Bernardi RC, Melo MCR, Schulten K. Enhanced sampling techniques in molecular dynamics simulations of biological systems. Biochim Biophys Acta 2015;1850:872-7. [PMID: 25450171 DOI: 10.1016/j.bbagen.2014.10.019] [Cited by in Crossref: 332] [Cited by in F6Publishing: 263] [Article Influence: 41.5] [Reference Citation Analysis]
24 Hénin J, Fiorin G, Chipot C, Klein ML. Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables. J Chem Theory Comput 2010;6:35-47. [PMID: 26614317 DOI: 10.1021/ct9004432] [Cited by in Crossref: 303] [Cited by in F6Publishing: 246] [Article Influence: 23.3] [Reference Citation Analysis]
25 Kordzadeh A, Ramazani Saadatabadi A, Hadi A. Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulation. Heliyon 2020;6:e05681. [PMID: 33344790 DOI: 10.1016/j.heliyon.2020.e05681] [Cited by in Crossref: 3] [Cited by in F6Publishing: 2] [Article Influence: 1.5] [Reference Citation Analysis]
26 Marracino P, Liberti M, Trapani E, Burnham CJ, Avena M, Garate JA, Apollonio F, English NJ. Human Aquaporin 4 Gating Dynamics under Perpendicularly-Oriented Electric-Field Impulses: A Molecular Dynamics Study. Int J Mol Sci 2016;17:E1133. [PMID: 27428954 DOI: 10.3390/ijms17071133] [Cited by in Crossref: 19] [Cited by in F6Publishing: 13] [Article Influence: 3.2] [Reference Citation Analysis]
27 Comer J, Schulten K, Chipot C. Calculation of Lipid-Bilayer Permeabilities Using an Average Force. J Chem Theory Comput 2014;10:554-64. [PMID: 26580032 DOI: 10.1021/ct400925s] [Cited by in Crossref: 48] [Cited by in F6Publishing: 43] [Article Influence: 6.9] [Reference Citation Analysis]
28 Jiang W, Lin YC, Botello-Smith W, Contreras JE, Harris AL, Maragliano L, Luo YL. Free energy and kinetics of cAMP permeation through connexin26 via applied voltage and milestoning. Biophys J 2021;120:2969-83. [PMID: 34214529 DOI: 10.1016/j.bpj.2021.06.024] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
29 Erimban S, Daschakraborty S. Translocation of a hydroxyl functionalized carbon dot across a lipid bilayer: an all-atom molecular dynamics simulation study. Phys Chem Chem Phys 2020;22:6335-50. [DOI: 10.1039/c9cp05999g] [Cited by in Crossref: 7] [Article Influence: 3.5] [Reference Citation Analysis]
30 Kosicka E, Lesicki A, Pieńkowska JR. Molluscan aquaporins: an overview, with some notes on their role in the entry into aestivation in gastropods. Molluscan Research 2020;40:101-11. [DOI: 10.1080/13235818.2020.1716442] [Cited by in Crossref: 5] [Cited by in F6Publishing: 2] [Article Influence: 2.5] [Reference Citation Analysis]
31 Kuan YC, Xu YB, Wang WC, Yang MT. Enantioselective synthesis of (R)-phenylephrine by Serratia marcescens BCRC10948 cells that homologously express SM_SDR. Enzyme Microb Technol 2018;110:14-9. [PMID: 29310851 DOI: 10.1016/j.enzmictec.2017.12.001] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.3] [Reference Citation Analysis]
32 Chen LY. Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations. Biophys Chem 2010;151:178-80. [PMID: 20573441 DOI: 10.1016/j.bpc.2010.05.014] [Cited by in Crossref: 8] [Cited by in F6Publishing: 9] [Article Influence: 0.7] [Reference Citation Analysis]
33 Wang Z, Yu T, Sang J, Zou X, Yan C, Zou X. Computation and Simulation of the Structural Characteristics of the Kidney Urea Transporter and Behaviors of Urea Transport. J Phys Chem B 2015;119:5124-31. [DOI: 10.1021/jp511300u] [Cited by in Crossref: 11] [Cited by in F6Publishing: 8] [Article Influence: 1.6] [Reference Citation Analysis]
34 Hajjar E, Kumar A, Ruggerone P, Ceccarelli M. Investigating reaction pathways in rare events simulations of antibiotics diffusion through protein channels. J Mol Model 2010;16:1701-8. [DOI: 10.1007/s00894-010-0698-4] [Cited by in Crossref: 10] [Cited by in F6Publishing: 11] [Article Influence: 0.8] [Reference Citation Analysis]
35 Peng G, Cho Y, Fu T, Yang M, Hsu W. Enantioselective synthesis of (S)-phenylephrine by recombinant Escherichia coli cells expressing the short-chain dehydrogenase/reductase gene from Serratia quinivorans BCRC 14811. Process Biochemistry 2013;48:1509-15. [DOI: 10.1016/j.procbio.2013.07.006] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 0.4] [Reference Citation Analysis]
36 Russell-Jones G. Intestinal receptor targeting for peptide delivery: an expert's personal perspective on reasons for failure and new opportunities. Ther Deliv 2011;2:1575-93. [PMID: 22833983 DOI: 10.4155/tde.11.129] [Cited by in Crossref: 21] [Cited by in F6Publishing: 19] [Article Influence: 2.1] [Reference Citation Analysis]
37 Pongprayoon P, Beckstein O, Wee CL, Sansom MS. Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate. Proc Natl Acad Sci U S A 2009;106:21614-8. [PMID: 19966228 DOI: 10.1073/pnas.0907315106] [Cited by in Crossref: 49] [Cited by in F6Publishing: 48] [Article Influence: 3.8] [Reference Citation Analysis]
38 Spinello A, de Almeida A, Casini A, Barone G. The inhibition of glycerol permeation through aquaglyceroporin-3 induced by mercury(II): A molecular dynamics study. Journal of Inorganic Biochemistry 2016;160:78-84. [DOI: 10.1016/j.jinorgbio.2015.11.027] [Cited by in Crossref: 20] [Cited by in F6Publishing: 18] [Article Influence: 3.3] [Reference Citation Analysis]
39 Yao J, Rock CO. Phosphatidic acid synthesis in bacteria. Biochim Biophys Acta 2013;1831:495-502. [PMID: 22981714 DOI: 10.1016/j.bbalip.2012.08.018] [Cited by in Crossref: 106] [Cited by in F6Publishing: 91] [Article Influence: 10.6] [Reference Citation Analysis]
40 Luo Y, Rossi AR, Harris AL. Computational Studies of Molecular Permeation through Connexin26 Channels. Biophys J 2016;110:584-99. [PMID: 26840724 DOI: 10.1016/j.bpj.2015.11.3528] [Cited by in Crossref: 15] [Cited by in F6Publishing: 14] [Article Influence: 3.0] [Reference Citation Analysis]
41 Kang M, Lam D, Discher DE, Loverde SM. Molecular Modeling of Block Copolymer Self-Assembly and Micellar Drug Delivery. In: Ouyang D, Smith SC, editors. Computational Pharmaceutics. Chichester: John Wiley & Sons, Ltd; 2015. pp. 53-80. [DOI: 10.1002/9781118573983.ch4] [Cited by in Crossref: 5] [Cited by in F6Publishing: 4] [Article Influence: 0.7] [Reference Citation Analysis]
42 Lee PH, Helms V. Identifying continuous pores in protein structures with PROPORES by computational repositioning of gating residues. Proteins 2012;80:421-32. [PMID: 22095919 DOI: 10.1002/prot.23204] [Cited by in Crossref: 9] [Cited by in F6Publishing: 8] [Article Influence: 0.8] [Reference Citation Analysis]
43 du Toit JP, Pott RWM. Transparent polyvinyl-alcohol cryogel as immobilisation matrix for continuous biohydrogen production by phototrophic bacteria. Biotechnol Biofuels 2020;13:105. [PMID: 32536970 DOI: 10.1186/s13068-020-01743-7] [Cited by in Crossref: 8] [Cited by in F6Publishing: 4] [Article Influence: 4.0] [Reference Citation Analysis]
44 Hu G, Cao Z, Xu S, Wang W, Wang J. Revealing the binding modes and the unbinding of 14-3-3σ proteins and inhibitors by computational methods. Sci Rep 2015;5:16481. [PMID: 26568041 DOI: 10.1038/srep16481] [Cited by in Crossref: 19] [Cited by in F6Publishing: 17] [Article Influence: 2.7] [Reference Citation Analysis]
45 Lee BL, Kuczera K, Middaugh CR, Jas GS. Permeation of the three aromatic dipeptides through lipid bilayers: Experimental and computational study. The Journal of Chemical Physics 2016;144:245103. [DOI: 10.1063/1.4954241] [Cited by in Crossref: 14] [Cited by in F6Publishing: 12] [Article Influence: 2.3] [Reference Citation Analysis]
46 Klepeis JL, Lindorff-larsen K, Dror RO, Shaw DE. Long-timescale molecular dynamics simulations of protein structure and function. Current Opinion in Structural Biology 2009;19:120-7. [DOI: 10.1016/j.sbi.2009.03.004] [Cited by in Crossref: 526] [Cited by in F6Publishing: 450] [Article Influence: 40.5] [Reference Citation Analysis]
47 Pothula KR, Solano CJ, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. Biochim Biophys Acta 2016;1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Cited by in Crossref: 37] [Cited by in F6Publishing: 32] [Article Influence: 5.3] [Reference Citation Analysis]
48 Haloi N, Vasan AK, Geddes EJ, Prasanna A, Wen PC, Metcalf WW, Hergenrother PJ, Tajkhorshid E. Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge. Chem Sci 2021;12:15028-44. [PMID: 34909143 DOI: 10.1039/d1sc04445a] [Reference Citation Analysis]
49 Paul TK, Taraphder S. Coordination Dynamics of Zinc Triggers the Rate Determining Proton Transfer in Human Carbonic Anhydrase II. ChemPhysChem 2020;21:1455-73. [DOI: 10.1002/cphc.202000177] [Cited by in Crossref: 5] [Cited by in F6Publishing: 1] [Article Influence: 2.5] [Reference Citation Analysis]
50 Hénin J, Shinoda W, Klein ML. Models for phosphatidylglycerol lipids put to a structural test. J Phys Chem B 2009;113:6958-63. [PMID: 19371035 DOI: 10.1021/jp900645z] [Cited by in Crossref: 24] [Cited by in F6Publishing: 22] [Article Influence: 1.8] [Reference Citation Analysis]
51 Oliva R, Calamita G, Thornton JM, Pellegrini-Calace M. Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity. Proc Natl Acad Sci U S A 2010;107:4135-40. [PMID: 20147624 DOI: 10.1073/pnas.0910632107] [Cited by in Crossref: 39] [Cited by in F6Publishing: 33] [Article Influence: 3.3] [Reference Citation Analysis]
52 Shaikh S, Wen PC, Enkavi G, Huang Z, Tajkhorshid E. Capturing Functional Motions of Membrane Channels and Transporters with Molecular Dynamics Simulation. J Comput Theor Nanosci 2010;7:2481-500. [PMID: 23710155 DOI: 10.1166/jctn.2010.1636] [Cited by in Crossref: 7] [Cited by in F6Publishing: 6] [Article Influence: 0.6] [Reference Citation Analysis]
53 Lindahl V, Gourdon P, Andersson M, Hess B. Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function. Sci Rep 2018;8:2995. [PMID: 29445244 DOI: 10.1038/s41598-018-21357-2] [Cited by in Crossref: 15] [Cited by in F6Publishing: 14] [Article Influence: 3.8] [Reference Citation Analysis]
54 Comer J, Gumbart JC, Hénin J, Lelièvre T, Pohorille A, Chipot C. The adaptive biasing force method: everything you always wanted to know but were afraid to ask. J Phys Chem B 2015;119:1129-51. [PMID: 25247823 DOI: 10.1021/jp506633n] [Cited by in Crossref: 210] [Cited by in F6Publishing: 161] [Article Influence: 26.3] [Reference Citation Analysis]
55 Chipot C. Frontiers in free-energy calculations of biological systems: WIREs Computational Molecular Science: frontiers in free-energy calculations. WIREs Comput Mol Sci 2014;4:71-89. [DOI: 10.1002/wcms.1157] [Cited by in Crossref: 92] [Cited by in F6Publishing: 43] [Article Influence: 10.2] [Reference Citation Analysis]
56 Comer J, Schulten K, Chipot C. Diffusive Models of Membrane Permeation with Explicit Orientational Freedom. J Chem Theory Comput 2014;10:2710-8. [PMID: 26586505 DOI: 10.1021/ct500209j] [Cited by in Crossref: 31] [Cited by in F6Publishing: 29] [Article Influence: 4.4] [Reference Citation Analysis]
57 Domene C, Furini S. Examining ion channel properties using free-energy methods. Methods Enzymol 2009;466:155-77. [PMID: 21609861 DOI: 10.1016/S0076-6879(09)66007-9] [Cited by in Crossref: 14] [Cited by in F6Publishing: 6] [Article Influence: 1.1] [Reference Citation Analysis]
58 Gumbart JC, Teo I, Roux B, Schulten K. Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion. J Am Chem Soc 2013;135:2291-7. [PMID: 23298280 DOI: 10.1021/ja310777k] [Cited by in Crossref: 37] [Cited by in F6Publishing: 32] [Article Influence: 4.1] [Reference Citation Analysis]
59 Wang Y, Shaikh SA, Tajkhorshid E. Exploring transmembrane diffusion pathways with molecular dynamics. Physiology (Bethesda) 2010;25:142-54. [PMID: 20551228 DOI: 10.1152/physiol.00046.2009] [Cited by in Crossref: 32] [Cited by in F6Publishing: 30] [Article Influence: 2.7] [Reference Citation Analysis]
60 Chen LY. Exploring the free-energy landscapes of biological systems with steered molecular dynamics. Phys Chem Chem Phys 2011;13:6176-83. [PMID: 21359274 DOI: 10.1039/c0cp02799e] [Cited by in Crossref: 24] [Cited by in F6Publishing: 22] [Article Influence: 2.2] [Reference Citation Analysis]
61 English NJ, Garate J. Near-microsecond human aquaporin 4 gating dynamics in static and alternating external electric fields: Non-equilibrium molecular dynamics. The Journal of Chemical Physics 2016;145:085102. [DOI: 10.1063/1.4961072] [Cited by in Crossref: 7] [Cited by in F6Publishing: 5] [Article Influence: 1.2] [Reference Citation Analysis]
62 Khalili-Araghi F, Gumbart J, Wen PC, Sotomayor M, Tajkhorshid E, Schulten K. Molecular dynamics simulations of membrane channels and transporters. Curr Opin Struct Biol 2009;19:128-37. [PMID: 19345092 DOI: 10.1016/j.sbi.2009.02.011] [Cited by in Crossref: 159] [Cited by in F6Publishing: 136] [Article Influence: 12.2] [Reference Citation Analysis]
63 Truelsen SF, Missel JW, Gotfryd K, Pedersen PA, Gourdon P, Lindorff-Larsen K, Hélix-Nielsen C. The role of water coordination in the pH-dependent gating of hAQP10. Biochim Biophys Acta Biomembr 2022;1864:183809. [PMID: 34699768 DOI: 10.1016/j.bbamem.2021.183809] [Reference Citation Analysis]
64 Wei C, Pohorille A. Permeation of membranes by ribose and its diastereomers. J Am Chem Soc 2009;131:10237-45. [PMID: 19621967 DOI: 10.1021/ja902531k] [Cited by in Crossref: 37] [Cited by in F6Publishing: 33] [Article Influence: 2.8] [Reference Citation Analysis]
65 Comer J, Chipot C, González-Nilo FD. Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations. J Chem Theory Comput 2013;9:876-82. [PMID: 26588731 DOI: 10.1021/ct300867e] [Cited by in Crossref: 45] [Cited by in F6Publishing: 40] [Article Influence: 5.0] [Reference Citation Analysis]
66 Elenewski JE, Hackett JC. Free Energy Landscape of the Retinol/Serum Retinol Binding Protein Complex: A Biological Host−Guest System. J Phys Chem B 2010;114:11315-22. [DOI: 10.1021/jp104103f] [Cited by in Crossref: 11] [Cited by in F6Publishing: 9] [Article Influence: 0.9] [Reference Citation Analysis]
67 Gumbart JC, Chipot C. Decrypting protein insertion through the translocon with free-energy calculations. Biochim Biophys Acta 2016;1858:1663-71. [PMID: 26896694 DOI: 10.1016/j.bbamem.2016.02.017] [Cited by in Crossref: 13] [Cited by in F6Publishing: 11] [Article Influence: 2.2] [Reference Citation Analysis]
68 Hu Y, Sinha SK, Patel S. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers. J Phys Chem B 2014;118:11973-92. [PMID: 25290376 DOI: 10.1021/jp504853t] [Cited by in Crossref: 13] [Cited by in F6Publishing: 9] [Article Influence: 1.6] [Reference Citation Analysis]
69 Chen E, Esquerra RM, Meléndez PA, Chandrasekaran SS, Kliger DS. Microviscosity in E. coli Cells from Time-Resolved Linear Dichroism Measurements. J Phys Chem B 2018;122:11381-9. [PMID: 30118225 DOI: 10.1021/acs.jpcb.8b07362] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.3] [Reference Citation Analysis]
70 Giwa A, Hasan S, Yousuf A, Chakraborty S, Johnson D, Hilal N. Biomimetic membranes: A critical review of recent progress. Desalination 2017;420:403-24. [DOI: 10.1016/j.desal.2017.06.025] [Cited by in Crossref: 57] [Cited by in F6Publishing: 27] [Article Influence: 11.4] [Reference Citation Analysis]
71 Burnham CJ, English NJ. Electropumping of Water Through Human Aquaporin 4 by Circularly Polarized Electric Fields: Dramatic Enhancement and Control Revealed by Non-Equilibrium Molecular Dynamics. J Phys Chem Lett 2017;8:4646-51. [PMID: 28905623 DOI: 10.1021/acs.jpclett.7b02323] [Cited by in Crossref: 7] [Cited by in F6Publishing: 7] [Article Influence: 1.4] [Reference Citation Analysis]
72 Kitchen P, Salman MM, Pickel SU, Jennings J, Törnroth-Horsefield S, Conner MT, Bill RM, Conner AC. Water channel pore size determines exclusion properties but not solute selectivity. Sci Rep 2019;9:20369. [PMID: 31889130 DOI: 10.1038/s41598-019-56814-z] [Cited by in Crossref: 14] [Cited by in F6Publishing: 12] [Article Influence: 4.7] [Reference Citation Analysis]
73 Ray D, Andricioaei I. Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA. Biophys J 2020;119:1568-79. [PMID: 32946766 DOI: 10.1016/j.bpj.2020.08.031] [Cited by in Crossref: 2] [Article Influence: 1.0] [Reference Citation Analysis]
74 Domene C, Barbini P, Furini S. Bias-Exchange Metadynamics Simulations: An Efficient Strategy for the Analysis of Conduction and Selectivity in Ion Channels. J Chem Theory Comput 2015;11:1896-906. [PMID: 26574394 DOI: 10.1021/ct501053x] [Cited by in Crossref: 27] [Cited by in F6Publishing: 26] [Article Influence: 4.5] [Reference Citation Analysis]
75 Bernardi M, Marracino P, Ghaani MR, Liberti M, Del Signore F, Burnham CJ, Gárate JA, Apollonio F, English NJ. Human aquaporin 4 gating dynamics under axially oriented electric-field impulses: A non-equilibrium molecular-dynamics study. J Chem Phys 2018;149:245102. [PMID: 30599740 DOI: 10.1063/1.5044665] [Cited by in Crossref: 15] [Cited by in F6Publishing: 6] [Article Influence: 5.0] [Reference Citation Analysis]
76 Chen LY, Bastien DA, Espejel HE. Determination of equilibrium free energy from nonequilibrium work measurements. Phys Chem Chem Phys 2010;12:6579-82. [PMID: 20463999 DOI: 10.1039/b926889h] [Cited by in Crossref: 23] [Cited by in F6Publishing: 22] [Article Influence: 1.9] [Reference Citation Analysis]
77 Wang D, Weng J, Wang W. Glycerol transport through the aquaglyceroporin GlpF: bridging dynamics and kinetics with atomic simulation. Chem Sci 2019;10:6957-65. [PMID: 31588262 DOI: 10.1039/c9sc01690b] [Cited by in Crossref: 4] [Article Influence: 1.3] [Reference Citation Analysis]
78 Reale R, English NJ, Garate J, Marracino P, Liberti M, Apollonio F. Human aquaporin 4 gating dynamics under and after nanosecond-scale static and alternating electric-field impulses: A molecular dynamics study of field effects and relaxation. The Journal of Chemical Physics 2013;139:205101. [DOI: 10.1063/1.4832383] [Cited by in Crossref: 49] [Cited by in F6Publishing: 33] [Article Influence: 5.4] [Reference Citation Analysis]
79 Hajjar E, Mahendran KR, Kumar A, Bessonov A, Petrescu M, Weingart H, Ruggerone P, Winterhalter M, Ceccarelli M. Bridging timescales and length scales: from macroscopic flux to the molecular mechanism of antibiotic diffusion through porins. Biophys J 2010;98:569-75. [PMID: 20159153 DOI: 10.1016/j.bpj.2009.10.045] [Cited by in Crossref: 35] [Cited by in F6Publishing: 36] [Article Influence: 2.9] [Reference Citation Analysis]