메뉴 건너뛰기




Volumn 20, Issue 8, 2015, Pages 13997-14021

A database of force-field parameters, dynamics, and properties of antimicrobial compounds

Author keywords

All atom force fields; Antimicrobial compounds; Molecular databases; Molecular dynamics simulations

Indexed keywords

ANTIINFECTIVE AGENT;

EID: 84941254912     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules200813997     Document Type: Article
Times cited : (48)

References (102)
  • 1
    • 77957231785 scopus 로고    scopus 로고
    • Induced fit, conformational selection and independent dynamic segments: An extended view of binding events
    • Csermely, P.; Palotai, R.; Nussinov, R. Induced fit, conformational selection and independent dynamic segments: An extended view of binding events. Trends Biochem. Sci. 2010, 35, 539-546.
    • (2010) Trends Biochem. Sci , vol.35 , pp. 539-546
    • Csermely, P.1    Palotai, R.2    Nussinov, R.3
  • 2
    • 84872859789 scopus 로고    scopus 로고
    • Molecular Recognition Ligand Association
    • Baron, R.; McCammon, J.A. Molecular Recognition and Ligand Association. Ann. Rev. Phys. Chem. 2013, 64, 151-175.
    • (2013) Ann. Rev. Phys. Chem , vol.64 , pp. 151-175
    • Baron, R.1    McCammon, J.A.2
  • 3
    • 1642357706 scopus 로고    scopus 로고
    • The many roles of computation in drug discovery
    • Jorgensen, W. The many roles of computation in drug discovery. Science 2004, 303, 1813-1818.
    • (2004) Science , vol.303 , pp. 1813-1818
    • Jorgensen, W.1
  • 5
    • 84872859789 scopus 로고    scopus 로고
    • Molecular Recognition and Ligand Association
    • Baron, R.; McCammon, J.A. Molecular Recognition and Ligand Association. Ann. Rev. Phys. Chem. 2013, 64, 151-175.
    • (2013) Ann. Rev. Phys. Chem , vol.64 , pp. 151-175
    • Baron, R.1    McCammon, J.A.2
  • 6
    • 84958160632 scopus 로고    scopus 로고
    • Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations
    • Vargiu, A.V.; Magistrato, A. Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations. ChemMedChem 2014, 9, 1966-1981.
    • (2014) ChemMedChem , vol.9 , pp. 1966-1981
    • Vargiu, A.V.1    Magistrato, A.2
  • 7
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr, D.D.; Nussinov, R.; Wright, P.E. The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol. 2009, 5, 789-796.
    • (2009) Nat. Chem. Biol , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 10
    • 84884931806 scopus 로고    scopus 로고
    • Twenty-Five Years of Nucleic Acid Simulations
    • Cheatham, T.E., III; Case, D.A. Twenty-Five Years of Nucleic Acid Simulations. Biopolymers 2013, 99, 969-977.
    • (2013) Biopolymers , vol.99 , pp. 969-977
    • Cheatham, T.E.1    Case, D.A.2
  • 12
    • 84905400486 scopus 로고    scopus 로고
    • Charged residues distribution modulates selectivity of the open state of human isoforms of the voltage dependent anion-selective channel
    • Amodeo, G.F.; Scorciapino, M.A.; Messina, A.; De Pinto, V.; Ceccarelli, M. Charged residues distribution modulates selectivity of the open state of human isoforms of the voltage dependent anion-selective channel. PLoS ONE 2014, 9, e103879.
    • (2014) PLoS ONE , vol.9 , pp. e103879
    • Amodeo, G.F.1    Scorciapino, M.A.2    Messina, A.3    De Pinto, V.4    Ceccarelli, M.5
  • 13
    • 38949151546 scopus 로고    scopus 로고
    • Molecular simulations of protein dynamics: New windows on mechanisms in biology
    • Dodson, G.G.; Lane, D.P.; Verma, C.S. Molecular simulations of protein dynamics: New windows on mechanisms in biology. EMBO Rep. 2008, 9, 144-150.
    • (2008) EMBO Rep , vol.9 , pp. 144-150
    • Dodson, G.G.1    Lane, D.P.2    Verma, C.S.3
  • 14
    • 84861367246 scopus 로고    scopus 로고
    • Biomolecular Simulation: A Computational Microscope for Molecular Biology
    • Dror, R.O.; Dirks, R.M.; Grossman, J.P.; Xu, H.; Shaw, D.E. Biomolecular Simulation: A Computational Microscope for Molecular Biology. Ann. Rev. Biophys. 2012, 41, 429-452.
    • (2012) Ann. Rev. Biophys , vol.41 , pp. 429-452
    • Dror, R.O.1    Dirks, R.M.2    Grossman, J.P.3    Xu, H.4    Shaw, D.E.5
  • 15
    • 85008253380 scopus 로고    scopus 로고
    • Significance of Molecular Dynamics Simulations for Life Sciences
    • Karplus, M.; Lavery, R. Significance of Molecular Dynamics Simulations for Life Sciences. Isr. J. Chem. 2014, 54, 1042-1051.
    • (2014) Isr. J. Chem , vol.54 , pp. 1042-1051
    • Karplus, M.1    Lavery, R.2
  • 16
    • 84934927811 scopus 로고    scopus 로고
    • The impact of molecular dynamics on drug design: Applications for the characterization of ligand-macromolecule complexes
    • Mortier, J.; Rakers, C.; Bermudez, M.; Murgueitio, M.S.; Riniker, S.; Wolber, G. The impact of molecular dynamics on drug design: Applications for the characterization of ligand-macromolecule complexes. Drug Discov. Today 2015, 20, 686-702.
    • (2015) Drug Discov. Today , vol.20 , pp. 686-702
    • Mortier, J.1    Rakers, C.2    Bermudez, M.3    Murgueitio, M.S.4    Riniker, S.5    Wolber, G.6
  • 18
    • 0012818236 scopus 로고
    • Testing and comparison of empirical force fields: Techniques and problems
    • Gunsteren, W.F.V., Weiner, P., Wilkinson, A.J., Eds.; ESCOM: Leiden, The Netherlands
    • Gelin, B.R. Testing and comparison of empirical force fields: Techniques and problems. In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications; Gunsteren, W.F.V., Weiner, P., Wilkinson, A.J., Eds.; ESCOM: Leiden, The Netherlands, 1993; Volume 2, pp. 127-146.
    • (1993) Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , vol.2 , pp. 127-146
    • Gelin, B.R.1
  • 20
    • 0034639970 scopus 로고    scopus 로고
    • A density functional normal mode calculation of a bacteriochlorophyll a derivative
    • Ceccarelli, M.; Lutz, M.; Marchi, M. A density functional normal mode calculation of a bacteriochlorophyll a derivative. J. Am. Chem. Soc. 2000, 122, 3532-3533.
    • (2000) J. Am. Chem. Soc , vol.122 , pp. 3532-3533
    • Ceccarelli, M.1    Lutz, M.2    Marchi, M.3
  • 21
    • 0038339489 scopus 로고    scopus 로고
    • Simulation and Modeling of the Rhodobacter sphaeroides Bacterial Reaction Center II: Primary Charge Separation
    • Ceccarelli, M.; Marchi, M. Simulation and Modeling of the Rhodobacter sphaeroides Bacterial Reaction Center II: Primary Charge Separation. J. Phys. Chem. B 2003, 107, 5630-5641.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 5630-5641
    • Ceccarelli, M.1    Marchi, M.2
  • 22
    • 84892963298 scopus 로고    scopus 로고
    • Assessing the accuracy of physical models used in protein-folding simulations: Quantitative evidence from long molecular dynamics simulations
    • Piana, S.; Klepeis, J.L.; Shaw, D.E. Assessing the accuracy of physical models used in protein-folding simulations: Quantitative evidence from long molecular dynamics simulations. Curr. Opin. Struct. Biol. 2014, 24, 98-105.
    • (2014) Curr. Opin. Struct. Biol , vol.24 , pp. 98-105
    • Piana, S.1    Klepeis, J.L.2    Shaw, D.E.3
  • 24
    • 84867820827 scopus 로고    scopus 로고
    • LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations
    • Schmidt, T.H.; Kandt, C. LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations. J. Chem. Inf. Mod. 2012, 52, 2657-2669.
    • (2012) J. Chem. Inf. Mod , vol.52 , pp. 2657-2669
    • Schmidt, T.H.1    Kandt, C.2
  • 26
    • 84916232194 scopus 로고    scopus 로고
    • AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations
    • Graen, T.; Hoefling, M.; Grubmueller, H. AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations. J. Chem. Theory Comput. 2014, 10, 5505-5512.
    • (2014) J. Chem. Theory Comput , vol.10 , pp. 5505-5512
    • Graen, T.1    Hoefling, M.2    Grubmueller, H.3
  • 29
    • 84860154396 scopus 로고    scopus 로고
    • (accessed on 20 July 2014).
    • AMBER Parameter Database. Available online: http://www.pharmacy.manchester.ac.uk/bryce/ amber/ (accessed on 20 July 2014).
    • AMBER Parameter Database
  • 30
    • 84941235455 scopus 로고    scopus 로고
    • (accessed on 30 November 2014).
    • Marvin 14.8.25.0. ChemAxon 2014. Available online: http://www.chemaxon.com (accessed on 30 November 2014).
    • Marvin 14.8.25.0. ChemAxon 2014
  • 33
    • 84899087499 scopus 로고    scopus 로고
    • TRANSLOCATION Project: How to Get Good Drugs into Bad Bugs
    • Stavenger, R.A.;Winterhalter, M. TRANSLOCATION Project: How to Get Good Drugs into Bad Bugs. Sci. Transl. Med. 2014, 6, 228ed7.
    • (2014) Sci. Transl. Med , vol.6 , pp. 228ed7
    • Stavenger, R.A.1    Winterhalter, M.2
  • 34
    • 23444456920 scopus 로고
    • Prevention of drug access to bacterial targets: Permeability barriers and active efflux
    • Nikaido, H. Prevention of drug access to bacterial targets: Permeability barriers and active efflux. Science 1994, 264, 382-388.
    • (1994) Science , vol.264 , pp. 382-388
    • Nikaido, H.1
  • 35
    • 52449131735 scopus 로고    scopus 로고
    • Physical insights into permeation of and resistance to antibiotics in bacteria
    • Ceccarelli, M.; Ruggerone, P. Physical insights into permeation of and resistance to antibiotics in bacteria. Curr. Drug Targ. 2008, 9, 779-788.
    • (2008) Curr. Drug Targ , vol.9 , pp. 779-788
    • Ceccarelli, M.1    Ruggerone, P.2
  • 38
    • 0033235339 scopus 로고    scopus 로고
    • Nobel Lecture: Electronic structure of matter-wave functions and density functionals
    • Kohn, W. Nobel Lecture: Electronic structure of matter-wave functions and density functionals. Rev. Mod. Phys. 1999, 71, 1253-1266.
    • (1999) Rev. Mod. Phys , vol.71 , pp. 1253-1266
    • Kohn, W.1
  • 39
    • 0000189651 scopus 로고
    • Density-functional thermochemistry III. the role of exact exchange
    • Becke, A.D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648-5652.
    • (1993) J. Chem. Phys , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 40
    • 33645716728 scopus 로고
    • Comparison of Density Functional and MP2 Calculations on the Water Monomer and Dimer
    • Kim, K.; Jordan, K.D. Comparison of Density Functional and MP2 Calculations on the Water Monomer and Dimer. J. Phys. Chem. 1994, 98, 10089-10094.
    • (1994) J. Phys. Chem , vol.98 , pp. 10089-10094
    • Kim, K.1    Jordan, K.D.2
  • 41
    • 0033549476 scopus 로고    scopus 로고
    • Quantum Chemical Models (Nobel Lecture).
    • Pople, J.A. Quantum Chemical Models (Nobel Lecture). Angew. Chem. Int. Ed. 1999, 38, 1894-1902.
    • (1999) Angew. Chem. Int. Ed , vol.38 , pp. 1894-1902
    • Pople J. ., A.1
  • 42
    • 33846871670 scopus 로고    scopus 로고
    • On-line database of the spectral properties of polycyclic aromatic hydrocarbons
    • Malloci, G.; Joblin, C.; Mulas, G. On-line database of the spectral properties of polycyclic aromatic hydrocarbons. Chem. Phys. 2007, 332, 353-359.
    • (2007) Chem. Phys , vol.332 , pp. 353-359
    • Malloci, G.1    Joblin, C.2    Mulas, G.3
  • 43
    • 79958771826 scopus 로고    scopus 로고
    • Electronic and optical properties of families of polycyclic aromatic hydrocarbons: A systematic (time-dependent) density functional theory study
    • Malloci, G.; Cappellini, G.; Mulas, G.; Mattoni, A. Electronic and optical properties of families of polycyclic aromatic hydrocarbons: A systematic (time-dependent) density functional theory study. Chem. Phys. 2011, 384, 19-27.
    • (2011) Chem. Phys , vol.384 , pp. 19-27
    • Malloci, G.1    Cappellini, G.2    Mulas, G.3    Mattoni, A.4
  • 44
    • 84961980477 scopus 로고    scopus 로고
    • Quantum Mechanical Continuum Solvation Models
    • Tomasi, J.; Mennucci, B.; Cammi, R. Quantum Mechanical Continuum Solvation Models. Chem. Rev. 2005, 105, 2999-3094.
    • (2005) Chem. Rev , vol.105 , pp. 2999-3094
    • Tomasi, J.1    Mennucci, B.2    Cammi, R.3
  • 45
    • 40549115627 scopus 로고    scopus 로고
    • Cclib: A library for package-independent computational chemistry algorithms
    • O'Boyle, N.M.; Tenderholt, A.L.; Langner, K.M. cclib: A library for package-independent computational chemistry algorithms. J. Comput. Chem. 2008, 29, 839-845.
    • (2008) J. Comput. Chem , vol.29 , pp. 839-845
    • O'Boyle, N.M.1    Tenderholt, A.L.2    Langner, K.M.3
  • 46
    • 78449275560 scopus 로고    scopus 로고
    • Gabedit - A graphical user interface for computational chemistry softwares
    • Allouche, A.R. Gabedit - A graphical user interface for computational chemistry softwares. J. Comput. Chem. 2011, 32, 174-182.
    • (2011) J. Comput. Chem , vol.32 , pp. 174-182
    • Allouche, A.R.1
  • 47
    • 84986468608 scopus 로고
    • An approach to computing electrostatic charges for molecules
    • Singh, U.C.; Kollman, P.A. An approach to computing electrostatic charges for molecules. J. Comput. Chem. 1984, 5, 129-145.
    • (1984) J. Comput. Chem , vol.5 , pp. 129-145
    • Singh, U.C.1    Kollman, P.A.2
  • 48
    • 84986513567 scopus 로고
    • Determining atom-centered monopoles from molecular electrostatic potentials. the need for high sampling density in formamide conformational analysis
    • Breneman, C.M.; Wiberg, K.B. Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J. Comput. Chem. 1990, 11, 361-373.
    • (1990) J. Comput. Chem , vol.11 , pp. 361-373
    • Breneman, C.M.1    Wiberg, K.B.2
  • 49
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
    • Bayly, C.I.; Cieplak, P.; Cornell, W.; Kollman, P.A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. J. Phys. Chem. 1993, 97, 10269-10280.
    • (1993) J. Phys. Chem , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.3    Kollman, P.A.4
  • 50
    • 33748538349 scopus 로고    scopus 로고
    • Automatic atom type and bond type perception in molecular mechanical calculations
    • Wang, J.; Wang, W.; Kollman, P.A.; Case, D.A. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graph. Model. 2006, 25, 247-260.
    • (2006) J. Mol. Graph. Model , vol.25 , pp. 247-260
    • Wang, J.1    Wang, W.2    Kollman, P.A.3    Case, D.A.4
  • 51
    • 37249091134 scopus 로고    scopus 로고
    • Computation of Octanol-Water Partition Coefficients by Guiding an Additive Model with Knowledge
    • Cheng, T.; Zhao, Y.; Li, X.; Lin, F.; Xu, Y.; Zhang, X.; Li, Y.; Wang, R.; Lai, L. Computation of Octanol-Water Partition Coefficients by Guiding an Additive Model with Knowledge. J. Chem. Inf. Model. 2007, 47, 2140-2148.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 2140-2148
    • Cheng, T.1    Zhao, Y.2    Li, X.3    Lin, F.4    Xu, Y.5    Zhang, X.6    Li, Y.7    Wang, R.8    Lai, L.9
  • 52
    • 65449186590 scopus 로고    scopus 로고
    • PLATINUM: A web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes
    • Pyrkov, T.V.; Chugunov, A.O.; Krylov, N.A.; Nolde, D.E.; Efremov, R.G. PLATINUM: A web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. Bioinformatics 2009, 25, 1201-1202.
    • (2009) Bioinformatics , vol.25 , pp. 1201-1202
    • Pyrkov, T.V.1    Chugunov, A.O.2    Krylov, N.A.3    Nolde, D.E.4    Efremov, R.G.5
  • 54
    • 49449085241 scopus 로고    scopus 로고
    • Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
    • Joung, I.S.; Cheatham, T.E. Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 2008, 112, 9020-9041.
    • (2008) J. Phys. Chem. B , vol.112 , pp. 9020-9041
    • Joung, I.S.1    Cheatham, T.E.2
  • 56
    • 0026869597 scopus 로고
    • Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N0-methylamide
    • Loncharich, R.J.; Brooks, B.R.; Pastor, R.W. Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N0-methylamide. Biopolymers 1992, 32, 523-535.
    • (1992) Biopolymers , vol.32 , pp. 523-535
    • Loncharich, R.J.1    Brooks, B.R.2    Pastor, R.W.3
  • 57
    • 84880022273 scopus 로고    scopus 로고
    • PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
    • Roe, D.R.; Cheatham, T.E. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. J. Chem. Theory Comput. 2013, 9, 3084-3095.
    • (2013) J. Chem. Theory Comput , vol.9 , pp. 3084-3095
    • Roe, D.R.1    Cheatham, T.E.2
  • 58
    • 40449084229 scopus 로고    scopus 로고
    • Effects of ion concentration on the hydrogen bonded structure of water in the vicinity of ions in aqueous NaCl solutions
    • Nag, A.; Chakraborty, D.; Chandra, A. Effects of ion concentration on the hydrogen bonded structure of water in the vicinity of ions in aqueous NaCl solutions. J. Chem. Sci. 2008, 120, 71-77.
    • (2008) J. Chem. Sci , vol.120 , pp. 71-77
    • Nag, A.1    Chakraborty, D.2    Chandra, A.3
  • 59
    • 4243422452 scopus 로고    scopus 로고
    • Effect of Environment on Hydrogen Bond Dynamics in Liquid Water
    • Luzar, A.; Chandler, D. Effect of Environment on Hydrogen Bond Dynamics in Liquid Water. Phys. Rev. Lett. 1996, 76, 928-931.
    • (1996) Phys. Rev. Lett , vol.76 , pp. 928-931
    • Luzar, A.1    Chandler, D.2
  • 60
    • 0002300553 scopus 로고    scopus 로고
    • Hydrogen-bond kinetics in liquid Water
    • Luzar, A.; Chandler, D. Hydrogen-bond kinetics in liquid Water. Nature 1996, 379, 55-57.
    • (1996) Nature , vol.379 , pp. 55-57
    • Luzar, A.1    Chandler, D.2
  • 61
    • 0001427242 scopus 로고    scopus 로고
    • Hydrogen bonded clusters in the liquid phase: I. Analysis of the velocity correlation function of water triplets
    • Sutmann, G.; Vallauri, R. Hydrogen bonded clusters in the liquid phase: I. Analysis of the velocity correlation function of water triplets. J. Phys. Condens. Matter 1998, 10, 9231-9240.
    • (1998) J. Phys. Condens. Matter , vol.10 , pp. 9231-9240
    • Sutmann, G.1    Vallauri, R.2
  • 62
    • 4243838224 scopus 로고    scopus 로고
    • Effects of Ion Atmosphere on Hydrogen-Bond Dynamics in Aqueous Electrolyte Solutions
    • Chandra, A. Effects of Ion Atmosphere on Hydrogen-Bond Dynamics in Aqueous Electrolyte Solutions. Phys. Rev. Lett. 2000, 85, 768-771.
    • (2000) Phys. Rev. Lett , vol.85 , pp. 768-771
    • Chandra, A.1
  • 63
    • 36649006642 scopus 로고    scopus 로고
    • Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
    • Shao, J.; Tanner, S.W.; Thompson, N.; Cheatham, T.E. Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms. J. Chem. Theory Comput. 2007, 3, 2312-2334.
    • (2007) J. Chem. Theory Comput , vol.3 , pp. 2312-2334
    • Shao, J.1    Tanner, S.W.2    Thompson, N.3    Cheatham, T.E.4
  • 66
    • 0001684030 scopus 로고
    • Shape of unperturbed linear polymers: Polypropylene
    • Theodorou, D.N.; Suter, U.W. Shape of unperturbed linear polymers: Polypropylene. Macromolecules 1985, 18, 1206-1214.
    • (1985) Macromolecules , vol.18 , pp. 1206-1214
    • Theodorou, D.N.1    Suter, U.W.2
  • 68
    • 79955574923 scopus 로고    scopus 로고
    • Version 1.3r1. The PyMOL Molecular Graphics System, Version 1.3, Schrödinger, LLC, Mannheim, Germany
    • The PyMOL Molecular Graphics System, Version 1.3r1. The PyMOL Molecular Graphics System, Version 1.3, Schrödinger, LLC, Mannheim, Germany.
    • The PyMOL Molecular Graphics System
  • 70
    • 77954911184 scopus 로고    scopus 로고
    • Molecular simulations reveal the mechanism and the determinants for ampicillin translocation through OmpF
    • Kumar, A.; Hajjar, E.; Ruggerone, P.; Ceccarelli, M. Molecular simulations reveal the mechanism and the determinants for ampicillin translocation through OmpF. J. Phys. Chem. B 2010, 114, 9608-9616.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 9608-9616
    • Kumar, A.1    Hajjar, E.2    Ruggerone, P.3    Ceccarelli, M.4
  • 73
    • 84869433336 scopus 로고    scopus 로고
    • Recognition of Imipenem and Meropenem by the RND-Transporter MexB Studied by Computer Simulations
    • Collu, F.; Vargiu, A.V.; Dreier, J.; Cascella, M.; Ruggerone, P. Recognition of Imipenem and Meropenem by the RND-Transporter MexB Studied by Computer Simulations. J. Am. Chem. Soc. 2012, 134, 19146-19158.
    • (2012) J. Am. Chem. Soc , vol.134 , pp. 19146-19158
    • Collu, F.1    Vargiu, A.V.2    Dreier, J.3    Cascella, M.4    Ruggerone, P.5
  • 74
    • 84874431455 scopus 로고    scopus 로고
    • Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations
    • Vargiu, A.V.; Nikaido, H. Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations. Proc. Natl. Acad. Sci. USA 2012, 109, 20637-20642.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 20637-20642
    • Vargiu, A.V.1    Nikaido, H.2
  • 75
    • 84907267776 scopus 로고    scopus 로고
    • Molecular Mechanism of MBX2319 Inhibition of Escherichia coli AcrB Multidrug Efflux Pump and Comparison with Other Inhibitors
    • Vargiu, A.V.; Ruggerone, P.; Opperman, T.J.; Nguyen, S.T.; Nikaido, H. Molecular Mechanism of MBX2319 Inhibition of Escherichia coli AcrB Multidrug Efflux Pump and Comparison with Other Inhibitors. Antimicrob. Agents Chemother. 2014, 58, 6224-6234.
    • (2014) Antimicrob. Agents Chemother , vol.58 , pp. 6224-6234
    • Vargiu, A.V.1    Ruggerone, P.2    Opperman, T.J.3    Nguyen, S.T.4    Nikaido, H.5
  • 78
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • Trott, O.; Olson, A.J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 2010, 31, 455-461.
    • (2010) J. Comput. Chem , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 79
    • 0038583687 scopus 로고    scopus 로고
    • Protein-protein docking with a reduced protein model accounting for side-chain flexibility
    • Zacharias, M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci. 2003, 12, 1271-1282.
    • (2003) Protein Sci , vol.12 , pp. 1271-1282
    • Zacharias, M.1
  • 80
    • 77951297973 scopus 로고    scopus 로고
    • Accounting for conformational changes during protein-protein docking
    • Zacharias, M. Accounting for conformational changes during protein-protein docking. Curr. Opin. Struct. Biol. 2010, 20, 180-186.
    • (2010) Curr. Opin. Struct. Biol , vol.20 , pp. 180-186
    • Zacharias, M.1
  • 81
    • 33645961330 scopus 로고    scopus 로고
    • Flexible protein-protein docking
    • Bonvin, A. Flexible protein-protein docking. Curr. Opin. Struct. Biol. 2006, 16, 194-200.
    • (2006) Curr. Opin. Struct. Biol , vol.16 , pp. 194-200
    • Bonvin, A.1
  • 82
    • 41949132916 scopus 로고    scopus 로고
    • Flexible ligand docking to multiple receptor conformations: A practical alternative
    • Totrov, M.; Abagyan, R. Flexible ligand docking to multiple receptor conformations: A practical alternative. Curr. Opin. Struct. Biol. 2008, 18, 178-184.
    • (2008) Curr. Opin. Struct. Biol , vol.18 , pp. 178-184
    • Totrov, M.1    Abagyan, R.2
  • 84
    • 63149162777 scopus 로고    scopus 로고
    • Managing protein flexibility in docking and its applications
    • B-Rao, C.; Subramanian, J.; Sharma, S.D. Managing protein flexibility in docking and its applications. Drug Discov. Today 2009, 14, 394-400.
    • (2009) Drug Discov. Today , vol.14 , pp. 394-400
    • B-Rao, C.1    Subramanian, J.2    Sharma, S.D.3
  • 85
    • 79952181220 scopus 로고    scopus 로고
    • Challenges and advances in computational docking: 2009 in review
    • Yuriev, E.; Agostino, M.; Ramsland, P.A. Challenges and advances in computational docking: 2009 in review. J. Mol. Recognit. 2011, 24, 149-164.
    • (2011) J. Mol. Recognit , vol.24 , pp. 149-164
    • Yuriev, E.1    Agostino, M.2    Ramsland, P.A.3
  • 86
    • 84871381838 scopus 로고    scopus 로고
    • Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design
    • Sinko, W.; Lindert, S.; McCammon, J.A. Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design. Chem. Biol. Drug Des. 2013, 81, 41-49.
    • (2013) Chem. Biol. Drug des , vol.81 , pp. 41-49
    • Sinko, W.1    Lindert, S.2    McCammon, J.A.3
  • 87
    • 34447275949 scopus 로고    scopus 로고
    • Ligand docking and structure-based virtual screening in drug discovery
    • Cavasotto, C.N.; Orry, A.J.W. Ligand docking and structure-based virtual screening in drug discovery. Curr. Opin. Struct. Biol. 2007, 7, 1006-1014.
    • (2007) Curr. Opin. Struct. Biol , vol.7 , pp. 1006-1014
    • Cavasotto, C.N.1    Orry, A.J.W.2
  • 88
    • 50249114683 scopus 로고    scopus 로고
    • An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
    • Amaro, R.E.; Baron, R.; McCammon, J.A. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J. Comput. -Aided Mol. Des. 2008, 22, 693-705.
    • (2008) J. Comput. -Aided Mol. des , vol.22 , pp. 693-705
    • Amaro, R.E.1    Baron, R.2    McCammon, J.A.3
  • 89
    • 79960204167 scopus 로고    scopus 로고
    • Effect of the F610A Mutation on Substrate Extrusion in the AcrB Transporter: Explanation and Rationale by Molecular Dynamics Simulations
    • Vargiu, A.V.; Collu, F.; Schulz, R.; Pos, K.M.; Zacharias, M.; Kleinekathöfer, U.; Ruggerone, P. Effect of the F610A Mutation on Substrate Extrusion in the AcrB Transporter: Explanation and Rationale by Molecular Dynamics Simulations. J. Am. Chem. Soc. 2011, 133, 10704-10707.
    • (2011) J. Am. Chem. Soc , vol.133 , pp. 10704-10707
    • Vargiu, A.V.1    Collu, F.2    Schulz, R.3    Pos, K.M.4    Zacharias, M.5    Kleinekathöfer, U.6    Ruggerone, P.7
  • 90
    • 84909641215 scopus 로고    scopus 로고
    • Molecular Mechanism of Viral Resistance to a Potent Non-nucleoside Inhibitor Unveiled by Molecular Simulations
    • Asthana, S.; Shukla, S.; Ruggerone, P.; Vargiu, A.V. Molecular Mechanism of Viral Resistance to a Potent Non-nucleoside Inhibitor Unveiled by Molecular Simulations. Biochemistry 2014, 53, 6941-6953.
    • (2014) Biochemistry , vol.53 , pp. 6941-6953
    • Asthana, S.1    Shukla, S.2    Ruggerone, P.3    Vargiu, A.V.4
  • 91
    • 84905399186 scopus 로고    scopus 로고
    • Switch-Loop Flexibility Affects Transport of Large Drugs by the Promiscuous AcrB Multidrug Efflux Transporter
    • Cha, H.J.; Müller, R.T.; Pos, K.M. Switch-Loop Flexibility Affects Transport of Large Drugs by the Promiscuous AcrB Multidrug Efflux Transporter. Antimicrob. Agents Chemother. 2014, 58, 4767-4772.
    • (2014) Antimicrob. Agents Chemother , vol.58 , pp. 4767-4772
    • Cha, H.J.1    Müller, R.T.2    Pos, K.M.3
  • 92
    • 84888251078 scopus 로고    scopus 로고
    • RND efflux pumps: Structural information translated into function and inhibition mechanisms
    • Ruggerone, P.; Murakami, S.; Pos, K.M.; Vargiu, A.V. RND efflux pumps: Structural information translated into function and inhibition mechanisms. Curr. Top. Med. Chem. 2013, 13, 3079-3100.
    • (2013) Curr. Top. Med. Chem , vol.13 , pp. 3079-3100
    • Ruggerone, P.1    Murakami, S.2    Pos, K.M.3    Vargiu, A.V.4
  • 93
    • 68949110351 scopus 로고    scopus 로고
    • Efflux-Mediated Drug Resistance in Bacteria An Update
    • Li, X.Z.; Nikaido, H. Efflux-Mediated Drug Resistance in Bacteria An Update. Drugs 2009, 69, 1555-1623.
    • (2009) Drugs , vol.69 , pp. 1555-1623
    • Li, X.Z.1    Nikaido, H.2
  • 94
    • 84911484514 scopus 로고    scopus 로고
    • Multidrug efflux pumps in Gram-negative bacteria and their role in antibiotic resistance
    • Blair, J.; Richmond, G.; Piddock, L. Multidrug efflux pumps in Gram-negative bacteria and their role in antibiotic resistance. Future Microbiol. 2014, 9, 1165-1177.
    • (2014) Future Microbiol , vol.9 , pp. 1165-1177
    • Blair, J.1    Richmond, G.2    Piddock, L.3
  • 96
    • 24044514016 scopus 로고    scopus 로고
    • Efflux-mediated antimicrobial resistance
    • Poole, K. Efflux-mediated antimicrobial resistance. J. Antimicrob. Chemother. 2005, 56, 20-51.
    • (2005) J. Antimicrob. Chemother , vol.56 , pp. 20-51
    • Poole, K.1
  • 97
    • 84856729230 scopus 로고    scopus 로고
    • Broad-specificity efflux pumps and their role in multidrug resistance of Gram-negative bacteria
    • Nikaido, H.; Pagés, J.M. Broad-specificity efflux pumps and their role in multidrug resistance of Gram-negative bacteria. FEMS Microbiol. Rev. 2012, 36, 340-363.
    • (2012) FEMS Microbiol. Rev , vol.36 , pp. 340-363
    • Nikaido, H.1    Pagés, J.M.2
  • 98
    • 84941235456 scopus 로고    scopus 로고
    • (accessed on 29 January 2014).
    • Chemicalize. ChemAxon 2014. Available online: http://www.chemicalize.org (accessed on 29 January 2014).
    • ChemAxon 2014
  • 99
    • 3142716857 scopus 로고    scopus 로고
    • Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
    • Hamelberg, D.; Mongan, J.; McCammon, J.A. Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. J. Chem. Phys. 2004, 120, 11919-11929.
    • (2004) J. Chem. Phys , vol.120 , pp. 11919-11929
    • Hamelberg, D.1    Mongan, J.2    McCammon, J.A.3
  • 100
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999, 314, 141-151.
    • (1999) Chem. Phys. Lett , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 101
    • 0037157317 scopus 로고    scopus 로고
    • On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
    • Fukunishi, H.;Watanabe, O.; Takada, S. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction. J. Chem. Phys. 2002, 116, 9058-9067.
    • (2002) J. Chem. Phys , vol.116 , pp. 9058-9067
    • Fukunishi, H.1    Watanabe, O.2    Takada, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.