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Volumn 49, Issue 8, 2009, Pages 1944-1951

Protein-ligand binding free energy calculation by the Smooth Reaction Path Generation (SRPG) method

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CROWN ETHERS; DISSOCIATION; LIGANDS; MOLECULAR DYNAMICS; PROTEINS; REACTION KINETICS;

EID: 69549138254     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci9002156     Document Type: Article
Times cited : (26)

References (45)
  • 2
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • DOI 10.1006/jmbi.1996.0477
    • (2) Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 267, 470-489. (Pubitemid 26335901)
    • (1996) Journal of Molecular Biology , vol.261 , Issue.3 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 3
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G.; Willet, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willet, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 4
    • 0032533791 scopus 로고    scopus 로고
    • Flexible docking using tabu search and an empirical estimate of binding affinity
    • Baxter, C. A.; Murray, C. W.; Clark, D. E.; Westhead, D. R.; Eldridge, M. D. Flexible docking using tabu search and an empirical estimate of binding affinity. Proteins 1998, 33, 367-382.
    • (1998) Proteins , vol.33 , pp. 367-382
    • Baxter, C.A.1    Murray, C.W.2    Clark, D.E.3    Westhead, D.R.4    Eldridge, M.D.5
  • 6
    • 84986522918 scopus 로고
    • ICM: A new method for structure modeling and design: Application to docking and structure prediction from the disordered native conformation
    • Abagyan, R.; Totrov, M.; Kuznetsov, D. ICM: A new method for structure modeling and design: Application to docking and structure prediction from the disordered native conformation. J. Comput. Chem. 1994, 15, 488-506.
    • (1994) J. Comput. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 7
    • 24944576105 scopus 로고    scopus 로고
    • Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening
    • DOI 10.1016/j.jmgm.2005.04.004, PII S1093326305000306
    • (7) Fukunishi, Y.; Mikami, Y.; Nakamura, H. Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening. J. Mol. Graph. Modell. 2005, 24, 34-45. (Pubitemid 41318116)
    • (2005) Journal of Molecular Graphics and Modelling , vol.24 , Issue.1 , pp. 34-45
    • Fukunishi, Y.1    Mikami, Y.2    Nakamura, H.3
  • 9
    • 33748594188 scopus 로고    scopus 로고
    • Multiple target screening method for robust and accurate in silico ligand screening
    • Fukunishi, Y.; Mikami, Y.; Kubota, S.; Nakamura, H. Multiple target screening method for robust and accurate in silico ligand screening. J. Mol. Graph. Modell. 2005, 25, 61-70.
    • (2005) J. Mol. Graph. Modell. , vol.25 , pp. 61-70
    • Fukunishi, Y.1    Mikami, Y.2    Kubota, S.3    Nakamura, H.4
  • 10
    • 17144383951 scopus 로고    scopus 로고
    • A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
    • DOI 10.1021/jm049314d
    • (10) Zhang, C.; Liu, S.; Zhu, Q.; Zhou, Y. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J. Med. Chem. 2005, 48, 2325-2335. (Pubitemid 40516427)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.7 , pp. 2325-2335
    • Zhang, C.1    Liu, S.2    Zhu, Q.3    Zhou, Y.4
  • 11
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge, I.; Martin, Y. C. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem. 1999, 42, 791-804.
    • (1999) J. Med. Chem. , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 13
    • 33846881144 scopus 로고    scopus 로고
    • Comparative evaluation of MMPBSA and XSCORE to compute binding free energy in XIAP-peptide complexes
    • DOI 10.1021/ci600412z
    • (13) Obiol-Pardo, C.; Rubio-Martinez, J. Comparative evaluation of MMPBSA and XSCORE to compute binding free energy in XIAPpeptide complexes. J. Chem. Inf. Model. 2007, 47, 134-142 (Pubitemid 46225569)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.1 , pp. 134-142
    • Obiol-Pardo, C.1    Rubio-Martinez, J.2
  • 14
    • 36649023306 scopus 로고    scopus 로고
    • Improving the accuracy of the linear interaction energy method for salvation free energies
    • Almlof, M.; Carlsson, J.; Åqvist, J. Improving the accuracy of the linear interaction energy method for salvation free energies. J. Chem. Theory. Comput. 2007, 3, 2162-2175.
    • (2007) J. Chem. Theory. Comput. , vol.3 , pp. 2162-2175
    • Almlof, M.1    Carlsson, J.2    Åqvist, J.3
  • 15
    • 33645923414 scopus 로고    scopus 로고
    • Linear interaction energy models for β-serectase (BACE) inhibitors: Role of van der Waals, electrostatic, and continuum-solvation terms
    • Tiunge, B. A.; Rajamani, R.; Baxter, E. W.; Reitz, A. B.; Reynolds, C. H. Linear interaction energy models for β-serectase (BACE) inhibitors: role of van der Waals, electrostatic, and continuum-solvation terms. J. Mol. Graph. Modell. 2006, 24, 475-484.
    • (2006) J. Mol. Graph. Modell. , vol.24 , pp. 475-484
    • Tiunge, B.A.1    Rajamani, R.2    Baxter, E.W.3    Reitz, A.B.4    Reynolds, C.H.5
  • 16
    • 0031637651 scopus 로고    scopus 로고
    • Ligand binding affinity prediction by linear interaction energy methods
    • (16) Hansson, T.; Marelius, J.; Åqvist, J. Ligand binding affinity prediction by linear interaction energy methods. J. Comput-Aided. Mol. Des. 1998, 12, 27-35. (Pubitemid 128513811)
    • (1998) Journal of Computer-Aided Molecular Design , vol.12 , Issue.1 , pp. 27-35
    • Hansson, T.1    Marelius, J.2    Aqvist, J.3
  • 17
    • 67649518877 scopus 로고    scopus 로고
    • Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase
    • Perdih, A.; Bren, U.; Solmajer, T. Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase. J. Mol. Model. 2009, 15, 983-996.
    • (2009) J. Mol. Model. , vol.15 , pp. 983-996
    • Perdih, A.1    Bren, U.2    Solmajer, T.3
  • 18
    • 33745472162 scopus 로고    scopus 로고
    • Free energy simulations of uncatalyzed DNA replication fidelity: Structure and stability of T·G and dTTP·G terminal DNA mismatches flanked by a single dangling nucleotide
    • DOI 10.1021/jp060292b
    • (18) Bren, U.; Martinek, V.; Florian, J. Free energy simulations of uncatalyzed DNA replication fidelity: structure and stability of T.G and dTTP'G terminal DNA mismatches flanked by a single dangling nucleotide. J. Phys. Chem. B 2006, 110, 10557-10566. (Pubitemid 43952953)
    • (2006) Journal of Physical Chemistry B , vol.110 , Issue.21 , pp. 10557-10566
    • Bren, U.1    Martinek, V.2    Florian, J.3
  • 19
    • 37349000545 scopus 로고    scopus 로고
    • Protein-inhibitor flexible docking by a multicanonical sampling: Native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others
    • DOI 10.1002/prot.21409
    • (19) Kamiya, N.; Yonezawa, Y.; Nakamura, H.; Higo, J. Protein-inhibitor flexible docking by a multicanonical sampling: Native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others. Proteins 2008, 70, 41-53. (Pubitemid 350293447)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.1 , pp. 41-53
    • Kamiya, N.1    Yonezawa, Y.2    Nakamura, H.3    Higo, J.4
  • 20
    • 0031592919 scopus 로고    scopus 로고
    • Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation
    • PII S0009261497010749
    • (20) Nakajima, N.; Higo, J.; Kidera, A.; Nakamura, H. Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation. Chem. Phys. Lett. 1997, 278, 297-301. (Pubitemid 127167026)
    • (1997) Chemical Physics Letters , vol.278 , Issue.4-6 , pp. 297-301
    • Nakajima, N.1    Higo, J.2    Kidera, A.3    Nakamura, H.4
  • 21
    • 0000106469 scopus 로고
    • Multicanonical algorithms for first-order phase transitions
    • Berg, B. A.; Neuhaus, T. Multicanonical algorithms for first-order phase transitions. Phys. Lett. B 1991, 267, 249-253.
    • (1991) Phys. Lett. B , vol.267 , pp. 249-253
    • Berg, B.A.1    Neuhaus, T.2
  • 22
    • 0030819348 scopus 로고    scopus 로고
    • Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides
    • (22) Nakajima, N.; Nakamura, H.; Kidera, A. Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides. J. Phys. Chem. B 1997, 101, 817-824. (Pubitemid 127627951)
    • (1997) Journal of Physical Chemistry B , vol.101 , Issue.5 , pp. 817-824
    • Nakajima, N.1    Nakamura, H.2    Kidera, A.3
  • 24
    • 0344121638 scopus 로고    scopus 로고
    • The filling potential method: A method for estimating the free energy surface for protein-ligand docking
    • Fukunishi, Y.; Mikami, Y.; Nakamura, H. The filling potential method: A method for estimating the free energy surface for protein-ligand docking. J. Phys. Chem. B 2003, 107, 13201-13210.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 13201-13210
    • Fukunishi, Y.1    Mikami, Y.2    Nakamura, H.3
  • 27
    • 0037036070 scopus 로고    scopus 로고
    • Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
    • DOI 10.1126/science.1071152
    • (27) Liphardt, J.; Dumont, S.; Smith, S. B.; Tinoco, I., Jr.; Bustamante, C. Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science 2002, 296, 1832-1835. (Pubitemid 34596263)
    • (2002) Science , vol.296 , Issue.5574 , pp. 1832-1835
    • Liphardt, J.1    Dumont, S.2    Smith, S.B.3    Tinoco Jr., I.4    Bustamante, C.5
  • 28
    • 0042885340 scopus 로고    scopus 로고
    • Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
    • Park, S.; Khalili-araghi, F.; Tajkhorshid, E.; Schulten, K. Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality. J. Chem. Phys. 2003, 119, 3559-3566.
    • (2003) J. Chem. Phys. , vol.119 , pp. 3559-3566
    • Park, S.1    Khalili-araghi, F.2    Tajkhorshid, E.3    Schulten, K.4
  • 31
    • 0029636784 scopus 로고
    • Mechanism and thermodynamics of ion selectivity in aqueous solution of 18-crown-6 ether: A molecular dynamics study
    • Dang, L. X. Mechanism and thermodynamics of ion selectivity in aqueous solution of 18-crown-6 ether: A molecular dynamics study. J. Am. Chem. Soc. 1995, 117, 6954-6960.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 6954-6960
    • Dang, L.X.1
  • 35
    • 0000026966 scopus 로고    scopus 로고
    • Explicit reversible integrators for extended systems dynamics
    • (35) Martyna, G. J.; Tuckerman, M E.; Tobias, D. J.; Klein, M. L. Explicit reversible integrators for extended systems dynamics. Mol. Phys. 1996, 87, 1117-1157. (Pubitemid 126453963)
    • (1996) Molecular Physics , vol.87 , Issue.5 , pp. 1117-1157
    • Martyna, G.J.1    Tuckerman, M.E.2    Tobias, D.J.3    Klein, M.L.4
  • 37
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 38
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems
    • Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 39
    • 0001313268 scopus 로고    scopus 로고
    • Potential of mean force calculation of solute molecules in water by a modified solvent-accessible surface method
    • (39) Fukunishi, Y.; Suzuki, M. Potential of mean force calculation of solute molecules in water by a modified solvent accessible surface method. J. Comput. Chem. 1997, 18, 1656-1663. (Pubitemid 127677979)
    • (1997) Journal of Computational Chemistry , vol.18 , Issue.13 , pp. 1656-1663
    • Fukunishi, Y.1    Suzuki, M.2
  • 41
    • 84984075110 scopus 로고
    • Fast atom bombardment mass spectrometry for crown ether-alkali cation stability constant determination
    • Bonas, G.; Bosso, C.; Vignon, M. R. Fast atom bombardment mass spectrometry for crown ether-alkali cation stability constant determination. Rapid Commun. Mass Spectrom. 1988, 2, 88-89.
    • (1988) Rapid Commun. Mass Spectrom. , vol.2 , pp. 88-89
    • Bonas, G.1    Bosso, C.2    Vignon, M.R.3
  • 42
    • 0000396658 scopus 로고
    • A fast algorithm for particle simulations
    • Greengard, L.; Rokhlin, V. A fast algorithm for particle simulations. J. Comput. Phys. 1987, 73, 325-348.
    • (1987) J. Comput. Phys. , vol.73 , pp. 325-348
    • Greengard, L.1    Rokhlin, V.2
  • 44
    • 39149130730 scopus 로고    scopus 로고
    • Surface plasmon resonance based assay for the detection and characterization of promiscuous inhibitors
    • DOI 10.1021/jm700952v
    • (44) Giannetti, A. M.; Koch, B. D.; Browner, M. F. Surface plasmon resonance based assay for the detection and characterization of promiscuous inhibitors. J. Med. Chem. 2008, 51, 574-580. (Pubitemid 351252285)
    • (2008) Journal of Medicinal Chemistry , vol.51 , Issue.3 , pp. 574-580
    • Giannetti, A.M.1    Koch, B.D.2    Browner, M.F.3
  • 45
    • 33748661856 scopus 로고
    • Overview of protein motions
    • Wiley: New York
    • Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Overview of protein motions. In Proteins; Wiley: New York, 1988; pp 14-21.
    • (1988) Proteins , pp. 14-21
    • Brooks III, C.L.1    Karplus, M.2    Pettitt, B.M.3


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