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For: Allen TW, Baştuğ T, Kuyucak S, Chung SH. Gramicidin A channel as a test ground for molecular dynamics force fields. Biophys J 2003;84:2159-68. [PMID: 12668425 PMCID: PMC1302783 DOI: 10.1016/s0006-3495(03)75022-x] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
Number Cited by Other Article(s)
1
Sağsöz ME, Sağlam B, Arslan K, Baştuğ T, Çavuş M, Puralı N. Structural, Functional and Molecular Dynamics Examination of a de novo cloned Otopetrin-like Proton Channel in crayfish. Cell Biochem Biophys 2024:10.1007/s12013-024-01310-z. [PMID: 38811473 DOI: 10.1007/s12013-024-01310-z] [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] [Accepted: 05/11/2024] [Indexed: 05/31/2024]
2
Choi I, Kim N, Song Y, Schatz GC, Hwang H. Extended kinetic lattice grand canonical Monte Carlo simulation method for transport of multicomponent ion mixtures through a model nanopore system. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
3
Zhang Y, Haider K, Kaur D, Ngo VA, Cai X, Mao J, Khaniya U, Zhu X, Noskov S, Lazaridis T, Gunner MR. Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416520420016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
4
Abel S, Marchi M. Deciphering the Structure of the Gramicidin A Channel in the Presence of AOT Reverse Micelles in Pentane Using Molecular Dynamics Simulations. J Phys Chem B 2020;124:11802-11818. [PMID: 33346653 DOI: 10.1021/acs.jpcb.0c08902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
5
Na S, Steinbrecher T, Koslowski T. Thermodynamic integration network approach to ion transport through protein channels: Perspectives and limits. J Comput Chem 2018;39:2539-2550. [DOI: 10.1002/jcc.25615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/27/2018] [Accepted: 09/03/2018] [Indexed: 12/20/2022]
6
Akhshi P, Wu G. Umbrella sampling molecular dynamics simulations reveal concerted ion movement through G-quadruplex DNA channels. Phys Chem Chem Phys 2018;19:11017-11025. [PMID: 28327752 DOI: 10.1039/c7cp01028a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
7
A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids. Molecules 2017;23:molecules23010077. [PMID: 29301229 PMCID: PMC6017617 DOI: 10.3390/molecules23010077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/26/2017] [Accepted: 12/28/2017] [Indexed: 11/18/2022]  Open
8
Zhekova HR, Ngo V, da Silva MC, Salahub D, Noskov S. Selective ion binding and transport by membrane proteins – A computational perspective. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
9
Chu H, Cao L, Peng X, Li G. Polarizable force field development for lipids and their efficient applications in membrane proteins. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1312] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
10
Peng X, Zhang Y, Chu H, Li Y, Zhang D, Cao L, Li G. Accurate Evaluation of Ion Conductivity of the Gramicidin A Channel Using a Polarizable Force Field without Any Corrections. J Chem Theory Comput 2016;12:2973-82. [DOI: 10.1021/acs.jctc.6b00128] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
11
Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions. Int J Mol Sci 2016;17:ijms17050692. [PMID: 27171075 PMCID: PMC4881518 DOI: 10.3390/ijms17050692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 04/26/2016] [Accepted: 04/26/2016] [Indexed: 11/16/2022]  Open
12
Setiadi J, Kuyucak S. Computational Investigation of the Effect of Lipid Membranes on Ion Permeation in Gramicidin A. MEMBRANES 2016;6:membranes6010020. [PMID: 26999229 PMCID: PMC4812426 DOI: 10.3390/membranes6010020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/08/2016] [Accepted: 03/08/2016] [Indexed: 06/05/2023]
13
Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015;1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
14
Liu X, Salahub DR. Molybdenum Carbide Nanocatalysts at Work in the in Situ Environment: A Density Functional Tight-Binding and Quantum Mechanical/Molecular Mechanical Study. J Am Chem Soc 2015;137:4249-59. [DOI: 10.1021/jacs.5b01494] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
15
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. ENTROPY 2013. [DOI: 10.3390/e16010163] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
16
Theoretical Investigation of the D83V Mutation within the Myocyte-Specific Enhancer Factor-2 Beta and Its Role in Cancer. ACTA ACUST UNITED AC 2013. [DOI: 10.1155/2013/313419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
17
Todorović M, Bowler DR, Gillan MJ, Miyazaki T. Density-functional theory study of gramicidin A ion channel geometry and electronic properties. J R Soc Interface 2013;10:20130547. [PMID: 24068174 PMCID: PMC3808544 DOI: 10.1098/rsif.2013.0547] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/03/2013] [Indexed: 01/29/2023]  Open
18
Timko J, Kuyucak S. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations. J Chem Phys 2013. [PMID: 23206041 DOI: 10.1063/1.4768247] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
19
Use of Molecular Dynamics for the Refinement of an Electrostatic Model for the In Silico Design of a Polymer Antidote for the Anticoagulant Fondaparinux. J Med Eng 2013;2013:487387. [PMID: 27006916 PMCID: PMC4782625 DOI: 10.1155/2013/487387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 06/06/2013] [Indexed: 11/30/2022]  Open
20
Molecular dynamics simulations of membrane proteins. Biophys Rev 2012;4:271-282. [PMID: 28510077 DOI: 10.1007/s12551-012-0084-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 06/06/2012] [Indexed: 10/28/2022]  Open
21
Kucukkal TG, Stuart SJ. Polarizable Molecular Dynamics Simulations of Aqueous Dipeptides. J Phys Chem B 2012;116:8733-40. [DOI: 10.1021/jp300528m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
22
Bauer BA, Patel S. Recent applications and developments of charge equilibration force fields for modeling dynamical charges in classical molecular dynamics simulations. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1153-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
23
Krishnamurthy V, Cornell B. Engineering aspects of biological ion channels--from biosensors to computational models for permeation. PROTOPLASMA 2012;249 Suppl 1:S3-S9. [PMID: 22038117 DOI: 10.1007/s00709-011-0333-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 10/04/2011] [Indexed: 05/31/2023]
24
Lucas TR, Bauer BA, Patel S. Charge equilibration force fields for molecular dynamics simulations of lipids, bilayers, and integral membrane protein systems. BIOCHIMICA ET BIOPHYSICA ACTA 2012;1818:318-29. [PMID: 21967961 PMCID: PMC4216680 DOI: 10.1016/j.bbamem.2011.09.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Revised: 09/13/2011] [Accepted: 09/14/2011] [Indexed: 01/06/2023]
25
Lucas TR, Bauer BA, Davis JE, Patel S. Molecular dynamics simulation of hydrated DPPC monolayers using charge equilibration force fields. J Comput Chem 2012;33:141-52. [PMID: 21997857 PMCID: PMC3488352 DOI: 10.1002/jcc.21927] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 06/24/2011] [Accepted: 07/30/2011] [Indexed: 12/21/2022]
26
Hilder TA, Gordon D, Chung SH. Computational modeling of transport in synthetic nanotubes. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2011;7:702-9. [DOI: 10.1016/j.nano.2011.02.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 02/12/2011] [Accepted: 02/21/2011] [Indexed: 01/06/2023]
27
Ganesan N, Bauer BA, Lucas TR, Patel S, Taufer M. Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs). J Comput Chem 2011;32:2958-73. [PMID: 21793003 DOI: 10.1002/jcc.21871] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 04/25/2011] [Accepted: 05/21/2011] [Indexed: 01/19/2023]
28
Baştuğ T, Kuyucak S. Comparative study of the energetics of ion permeation in Kv1.2 and KcsA potassium channels. Biophys J 2011;100:629-636. [PMID: 21281577 DOI: 10.1016/j.bpj.2010.12.3718] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 12/16/2010] [Accepted: 12/20/2010] [Indexed: 11/18/2022]  Open
29
Giorgino T, De Fabritiis G. A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A. J Chem Theory Comput 2011;7:1943-50. [PMID: 26596455 DOI: 10.1021/ct100707s] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
30
Li Y, Andersen OS, Roux B. Energetics of double-ion occupancy in the gramicidin A channel. J Phys Chem B 2011;114:13881-8. [PMID: 20939567 DOI: 10.1021/jp105820u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
31
Calderon CP. Estimation and Inference of Diffusion Coefficients in Complex Biomolecular Environments. J Chem Theory Comput 2011;7:280-90. [DOI: 10.1021/ct1004966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
32
Cerutti DS, Freddolino PL, Duke RE, Case DA. Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water models. J Phys Chem B 2011;114:12811-24. [PMID: 20860388 DOI: 10.1021/jp105813j] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
33
Hilder TA, Gordon D, Chung SH. Synthetic chloride-selective carbon nanotubes examined by using molecular and stochastic dynamics. Biophys J 2010;99:1734-42. [PMID: 20858417 PMCID: PMC2941003 DOI: 10.1016/j.bpj.2010.06.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 06/09/2010] [Accepted: 06/11/2010] [Indexed: 11/19/2022]  Open
34
The gramicidin channel ion permeation free-energy profile: direct and indirect effects of CHARMM force field improvements. Interdiscip Sci 2010;1:113-27. [PMID: 20084184 DOI: 10.1007/s12539-009-0025-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
35
Timko J, Bucher D, Kuyucak S. Dissociation of NaCl in water from ab initio molecular dynamics simulations. J Chem Phys 2010;132:114510. [DOI: 10.1063/1.3360310] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
36
Bahar I, Lezon TR, Bakan A, Shrivastava IH. Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev 2010;110:1463-97. [PMID: 19785456 PMCID: PMC2836427 DOI: 10.1021/cr900095e] [Citation(s) in RCA: 377] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
37
CALDERON CHRISTOPHERP, MARTINEZ JOSUEG, CARROLL RAYMONDJ, SORENSEN DANNYC. P-SPLINES USING DERIVATIVE INFORMATION. MULTISCALE MODELING & SIMULATION : A SIAM INTERDISCIPLINARY JOURNAL 2010;8:1562-1580. [PMID: 21691592 PMCID: PMC3117255 DOI: 10.1137/090768102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
38
Mustafa M, Henderson DJ, Busath DD. Free-energy profiles for ions in the influenza M2-TMD channel. Proteins 2009;76:794-807. [PMID: 19296508 DOI: 10.1002/prot.22376] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
39
Gordon D, Krishnamurthy V, Chung SH. Generalized Langevin models of molecular dynamics simulations with applications to ion channels. J Chem Phys 2009;131:134102. [DOI: 10.1063/1.3233945] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
40
Nielsen CH. Biomimetic membranes for sensor and separation applications. Anal Bioanal Chem 2009;395:697-718. [DOI: 10.1007/s00216-009-2960-0] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 07/02/2009] [Accepted: 07/07/2009] [Indexed: 01/04/2023]
41
Davis JE, Patel S. Charge equilibration force fields for lipid environments: applications to fully hydrated DPPC bilayers and DMPC-embedded gramicidin A. J Phys Chem B 2009;113:9183-96. [PMID: 19526999 PMCID: PMC2746983 DOI: 10.1021/jp901088g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
42
Bucher D, Kuyucak S. Importance of water polarization for ion permeation in narrow pores. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.06.069] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
43
Chen PC, Kuyucak S. Mechanism and energetics of charybdotoxin unbinding from a potassium channel from molecular dynamics simulations. Biophys J 2009;96:2577-88. [PMID: 19348743 DOI: 10.1016/j.bpj.2008.12.3952] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 12/10/2008] [Accepted: 12/15/2008] [Indexed: 10/20/2022]  Open
44
Mustafa M, Henderson DJ, Busath DD. Computational studies of gramicidin permeation: an entry way sulfonate enhances cation occupancy at entry sites. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009;1788:1404-12. [PMID: 19361485 DOI: 10.1016/j.bbamem.2009.03.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/15/2009] [Accepted: 03/29/2009] [Indexed: 11/15/2022]
45
Davis JE, Rahaman O, Patel S. Molecular dynamics simulations of a DMPC bilayer using nonadditive interaction models. Biophys J 2009;96:385-402. [PMID: 19167291 DOI: 10.1016/j.bpj.2008.09.048] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Accepted: 09/22/2008] [Indexed: 10/21/2022]  Open
46
Siu SWI, Böckmann RA. Low Free Energy Barrier for Ion Permeation Through Double-Helical Gramicidin. J Phys Chem B 2009;113:3195-202. [DOI: 10.1021/jp810302k] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
47
Wang YT, Su ZY, Liao JM, Chen CL. Potential of mean force for Syrian hamster prion epitope protein--monoclonal fab 3f4 antibody interaction studies. Eur J Med Chem 2008;44:3504-8. [PMID: 19304354 DOI: 10.1016/j.ejmech.2008.12.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Revised: 08/27/2008] [Accepted: 12/17/2008] [Indexed: 10/21/2022]
48
Bucher D, Kuyucak S. Polarization of Water in the First Hydration Shell of K+ and Ca2+ Ions. J Phys Chem B 2008;112:10786-90. [DOI: 10.1021/jp804694u] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
49
Baştuğ T, Chen PC, Patra SM, Kuyucak S. Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling. J Chem Phys 2008;128:155104. [PMID: 18433285 DOI: 10.1063/1.2904461] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
50
Baştuğ T, Kuyucak S. Response to “Comment on ‘Free energy simulations of single and double ion occupancy in gramicidin A’ ” [J. Chem. Phys. 128, 227101 (2008)]. J Chem Phys 2008. [DOI: 10.1063/1.2931571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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