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Volumn 3, Issue 6, 2007, Pages 2312-2334

Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms

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EID: 36649006642     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct700119m     Document Type: Article
Times cited : (712)

References (116)
  • 1
    • 0020200718 scopus 로고
    • Molecular dynamics: Perspective for complex systems
    • van Gunsteren, W. F.; Berendsen, H. J. Molecular dynamics: perspective for complex systems. Biochem. Soc. Trans. 1982, 10, 301-305.
    • (1982) Biochem. Soc. Trans , vol.10 , pp. 301-305
    • van Gunsteren, W.F.1    Berendsen, H.J.2
  • 2
    • 0020480264 scopus 로고
    • Protein dynamics in solution and in a crystalline environment: A molecular dynamics study
    • van Gunsteren, W. F.; Karplus, M. Protein dynamics in solution and in a crystalline environment: a molecular dynamics study. Biochemistry 1982, 21, 2259-2274.
    • (1982) Biochemistry , vol.21 , pp. 2259-2274
    • van Gunsteren, W.F.1    Karplus, M.2
  • 5
    • 0021104775 scopus 로고
    • Molecular dynamics of native protein: I. Computer simulation of trajectories
    • Levitt, M. Molecular dynamics of native protein: I. Computer simulation of trajectories. J. Mol. Biol. 1983, 168, 595-617.
    • (1983) J. Mol. Biol , vol.168 , pp. 595-617
    • Levitt, M.1
  • 6
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus, M.; McCammon, J. A. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 2002, 9, 646-652.
    • (2002) Nat. Struct. Biol , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 7
    • 0033654654 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids
    • Cheatham, T. E., III; Kollman, P. A. Molecular dynamics simulation of nucleic acids. Ann. Rev. Phys. Chem. 2000, 51, 435-471.
    • (2000) Ann. Rev. Phys. Chem , vol.51 , pp. 435-471
    • Cheatham III, T.E.1    Kollman, P.A.2
  • 8
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan, Y.; Kollman, P. A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998, 282, 740-744.
    • (1998) Science , vol.282 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 11
    • 2942547665 scopus 로고    scopus 로고
    • Simulation and modeling of nucleic acid structure, dynamics and interactions
    • Cheatham, T. E., III Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol. 2004, 14, 360-367.
    • (2004) Curr. Opin. Struct. Biol , vol.14 , pp. 360-367
    • Cheatham III, T.E.1
  • 12
    • 1942456697 scopus 로고    scopus 로고
    • Recent advances in the development and application of implicit solvent models in biomolecule simulations
    • Feig, M.; Brooks, C. L., III Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 2004, 14, 217-224.
    • (2004) Curr. Opin. Struct. Biol , vol.14 , pp. 217-224
    • Feig, M.1    Brooks III, C.L.2
  • 13
    • 0242443692 scopus 로고    scopus 로고
    • Protein simulation and drug design
    • Wong, C. F.; McCammon, J. A. Protein simulation and drug design. Adv. Protein Chem. 2003, 66, 87-121.
    • (2003) Adv. Protein Chem , vol.66 , pp. 87-121
    • Wong, C.F.1    McCammon, J.A.2
  • 14
    • 33846512402 scopus 로고    scopus 로고
    • Rueda, D.; Ferrer-Costa, C.; Meyer, T.; Perez, A.; Camps, J.; Hospital, A.; Gelpi, J. L.; Orozco, M. A consensus view of protein dynamics. Proc. Natl. Acad. Sci. 2007, 104, 796-801.
    • Rueda, D.; Ferrer-Costa, C.; Meyer, T.; Perez, A.; Camps, J.; Hospital, A.; Gelpi, J. L.; Orozco, M. A consensus view of protein dynamics. Proc. Natl. Acad. Sci. 2007, 104, 796-801.
  • 15
    • 0036280693 scopus 로고    scopus 로고
    • Protein and peptide folding explored with molecular simulations
    • Brooks, C. I. Protein and peptide folding explored with molecular simulations. Acc. Chem. Res. 2002, 35, 447-454.
    • (2002) Acc. Chem. Res , vol.35 , pp. 447-454
    • Brooks, C.I.1
  • 16
    • 0036280655 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the protein unfolding/folding reaction
    • Daggett, V. Molecular dynamics simulations of the protein unfolding/folding reaction. Acc. Chem. Res. 2002, 35, 422-449.
    • (2002) Acc. Chem. Res , vol.35 , pp. 422-449
    • Daggett, V.1
  • 17
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • Simmerling, C.; Strockbine, B.; Roitberg, A. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 2002, 124, 11258-11259.
    • (2002) J. Am. Chem. Soc , vol.124 , pp. 11258-11259
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.3
  • 19
    • 33745932337 scopus 로고    scopus 로고
    • The unfolded state of the villin headpiece helical subdomain: Computational studies of the role of locally stabilized structure
    • Wickstrom, L.; Okur, A.; Song, K.; Hornak, V.; Raleigh, D. P.; Simmerling, C. L. The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure. J. Mol. Biol. 2006, 360, 1094-1107.
    • (2006) J. Mol. Biol , vol.360 , pp. 1094-1107
    • Wickstrom, L.1    Okur, A.2    Song, K.3    Hornak, V.4    Raleigh, D.P.5    Simmerling, C.L.6
  • 20
    • 33846381622 scopus 로고    scopus 로고
    • Direct observation of microscopic reversibility in single-molecule protein folding
    • Day, R.; Daggett, V. Direct observation of microscopic reversibility in single-molecule protein folding. J. Mol. Biol. 2006, 366, 677-686.
    • (2006) J. Mol. Biol , vol.366 , pp. 677-686
    • Day, R.1    Daggett, V.2
  • 21
    • 33750468665 scopus 로고    scopus 로고
    • Sampling the multiple folding mechanisms of Trp-cage in explicit solvent
    • Juraszek, J.; Bolhuis, P. G. Sampling the multiple folding mechanisms of Trp-cage in explicit solvent. Proc. Natl. Acad. Sci. 2006, 103, 15859-15864.
    • (2006) Proc. Natl. Acad. Sci , vol.103 , pp. 15859-15864
    • Juraszek, J.1    Bolhuis, P.G.2
  • 22
    • 33750060447 scopus 로고    scopus 로고
    • Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields
    • Eleftheriou, M.; Germain, R. S.; Royyuru, A. K.; Zhou, R. Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields. J. Am. Chem. Soc. 2006, 128, 13388-13395.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 13388-13395
    • Eleftheriou, M.1    Germain, R.S.2    Royyuru, A.K.3    Zhou, R.4
  • 23
    • 33847021237 scopus 로고    scopus 로고
    • Cooperative folding mechanism of a beta-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation
    • Yoda, T.; Sugita, Y.; Okamoto, Y. Cooperative folding mechanism of a beta-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation. Proteins 2007, 66, 846-859.
    • (2007) Proteins , vol.66 , pp. 846-859
    • Yoda, T.1    Sugita, Y.2    Okamoto, Y.3
  • 24
    • 33846324298 scopus 로고    scopus 로고
    • The structure of the Alzheimer, amyloid beta 10-35 peptide probed through replica-exchange molecular dynamics simulations in explicit solvent
    • Baumketner, A.; Shea, J. E. The structure of the Alzheimer, amyloid beta 10-35 peptide probed through replica-exchange molecular dynamics simulations in explicit solvent. J. Mol. Biol. 2007, 366, 275-285.
    • (2007) J. Mol. Biol , vol.366 , pp. 275-285
    • Baumketner, A.1    Shea, J.E.2
  • 25
    • 33947252405 scopus 로고    scopus 로고
    • Chen, H. F.; Luo, R. Binding induced folding in p53-MDM2 complex. J. Am. Chem. Soc. 2007, 129, 2930-2937.
    • Chen, H. F.; Luo, R. Binding induced folding in p53-MDM2 complex. J. Am. Chem. Soc. 2007, 129, 2930-2937.
  • 26
    • 33847254549 scopus 로고    scopus 로고
    • Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: On the structure and possible role of internal water
    • Paschek, D.; Nymeyer, H.; Garcia, A. E. Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water. J. Struct. Biol. 2007, 157, 524-533.
    • (2007) J. Struct. Biol , vol.157 , pp. 524-533
    • Paschek, D.1    Nymeyer, H.2    Garcia, A.E.3
  • 27
    • 33947408015 scopus 로고    scopus 로고
    • Understanding the folding and stability of a zinc finger-based full sequence design protein with replica exchange molecular dynamics simulations
    • Li, W.; Zhang, J.; Wang, W. Understanding the folding and stability of a zinc finger-based full sequence design protein with replica exchange molecular dynamics simulations. Proteins 2007, 67, 338-349.
    • (2007) Proteins , vol.67 , pp. 338-349
    • Li, W.1    Zhang, J.2    Wang, W.3
  • 28
    • 33846106377 scopus 로고    scopus 로고
    • Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent
    • Periole, X.; Mark, A. E. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent. J. Chem. Phys. 2007, 126, 014903.
    • (2007) J. Chem. Phys , vol.126 , pp. 014903
    • Periole, X.1    Mark, A.E.2
  • 29
    • 34249930405 scopus 로고    scopus 로고
    • Protein-folding dynamics: Overview of molecular simulation techniques
    • Scheraga, H. A.; Khalili, M.; Liwo, A. Protein-folding dynamics: overview of molecular simulation techniques. Ann. Rev. Phys. Chem. 2007, 58, 57-83.
    • (2007) Ann. Rev. Phys. Chem , vol.58 , pp. 57-83
    • Scheraga, H.A.1    Khalili, M.2    Liwo, A.3
  • 30
    • 0037442584 scopus 로고    scopus 로고
    • Molecular dynamics simulations and thermodynamic analysis of DNA-drug complexes. Minor groove binding between 4′,6-diamidino-2-phenylindole (DAPI) and DNA duplexes in solution
    • Spackova, N.; Cheatham, T. E., III; Ryjacek, F.; Lankas, F.; van Meervelt, L.; Hobza, P.; Sponer, J. Molecular dynamics simulations and thermodynamic analysis of DNA-drug complexes. Minor groove binding between 4′,6-diamidino-2-phenylindole (DAPI) and DNA duplexes in solution. J. Am. Chem. Soc. 2003, 125, 1759-1769.
    • (2003) J. Am. Chem. Soc , vol.125 , pp. 1759-1769
    • Spackova, N.1    Cheatham III, T.E.2    Ryjacek, F.3    Lankas, F.4    van Meervelt, L.5    Hobza, P.6    Sponer, J.7
  • 31
    • 33750337737 scopus 로고    scopus 로고
    • Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism
    • Bui, J. M.; McCammon, J. A. Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism. Proc. Natl. Acad. Sci. 2006, 103, 15451-15456.
    • (2006) Proc. Natl. Acad. Sci , vol.103 , pp. 15451-15456
    • Bui, J.M.1    McCammon, J.A.2
  • 32
    • 33748513468 scopus 로고    scopus 로고
    • Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes
    • Lu, Y.; Yang, C. Y.; Wang, S. Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes. J. Am. Chem. Soc. 2006, 128, 11830-11839.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 11830-11839
    • Lu, Y.1    Yang, C.Y.2    Wang, S.3
  • 33
    • 33748442331 scopus 로고    scopus 로고
    • A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method
    • Xu, Y.; Wang, R. A computational analysis of the binding affinities of FKBP12 inhibitors using the MM-PB/SA method. Proteins 2006, 64, 1058-1068.
    • (2006) Proteins , vol.64 , pp. 1058-1068
    • Xu, Y.1    Wang, R.2
  • 34
    • 34248545958 scopus 로고    scopus 로고
    • A computational model of the inhibition of Mycobacterium, tuberculosis ATPase by a new drug candidate R207910
    • de Jonge, M. R.; Koymans, L. H.; Guillemont, J. E.; Koul, A.; Andries, K. A computational model of the inhibition of Mycobacterium, tuberculosis ATPase by a new drug candidate R207910. Proteins 2007, 67, 971-980.
    • (2007) Proteins , vol.67 , pp. 971-980
    • de Jonge, M.R.1    Koymans, L.H.2    Guillemont, J.E.3    Koul, A.4    Andries, K.5
  • 35
    • 34247238312 scopus 로고    scopus 로고
    • Mechanism of drug resistance due to N88S in CRF01_AE HIV-1 protease, analyzed by molecular dynamics simulations
    • Ode, H.; Matsuyama, S.; Hata, M.; Hoshino, T.; Kakizawa, J.; Sugiura, W. Mechanism of drug resistance due to N88S in CRF01_AE HIV-1 protease, analyzed by molecular dynamics simulations. J. Med. Chem. 2007, 50, 1768-1777.
    • (2007) J. Med. Chem , vol.50 , pp. 1768-1777
    • Ode, H.1    Matsuyama, S.2    Hata, M.3    Hoshino, T.4    Kakizawa, J.5    Sugiura, W.6
  • 36
    • 32244437816 scopus 로고    scopus 로고
    • HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations
    • Hornak, V.; Okur, A.; Rizzo, R. C.; Simmerling, C. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc. Natl. Acad. Sci. 2006, 103, 915-920.
    • (2006) Proc. Natl. Acad. Sci , vol.103 , pp. 915-920
    • Hornak, V.1    Okur, A.2    Rizzo, R.C.3    Simmerling, C.4
  • 37
    • 33644948688 scopus 로고    scopus 로고
    • HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state
    • Hornak, V.; Okur, A.; Rizzo, R. C.; Simmerling, C. HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state. J. Am. Chem. Soc. 2006, 128, 2812-2813.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 2812-2813
    • Hornak, V.1    Okur, A.2    Rizzo, R.C.3    Simmerling, C.4
  • 38
    • 33749259954 scopus 로고    scopus 로고
    • Kinking occurs during molecular dynamics simulations of small DNA minicircles
    • Lankas, F.; Lavery, R.; Maddocks, J. H. Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure 2006, 14, 1527-1534.
    • (2006) Structure , vol.14 , pp. 1527-1534
    • Lankas, F.1    Lavery, R.2    Maddocks, J.H.3
  • 39
    • 34250860701 scopus 로고    scopus 로고
    • Theoretical study of large conformational transitions in DNA: The B < - > A conformational change in water and ethanol/water
    • Noy, A.; Perez, A.; Laughton, C. A.; Orozco, M. Theoretical study of large conformational transitions in DNA: the B < - > A conformational change in water and ethanol/water. Nucl. Acids Res. 2007, 35, 3330-3338.
    • (2007) Nucl. Acids Res , vol.35 , pp. 3330-3338
    • Noy, A.1    Perez, A.2    Laughton, C.A.3    Orozco, M.4
  • 40
    • 34247860779 scopus 로고    scopus 로고
    • Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations
    • van der Vaart, A.; Karplus, M. Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations. J. Chem. Phys. 2007, 126, 164106.
    • (2007) J. Chem. Phys , vol.126 , pp. 164106
    • van der Vaart, A.1    Karplus, M.2
  • 41
    • 34247339716 scopus 로고    scopus 로고
    • Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states
    • Noe, F.; Horenko, I.; Schutte, C.; Smith, J. C. Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states. J. Chem. Phys. 2007, 126, 155102.
    • (2007) J. Chem. Phys , vol.126 , pp. 155102
    • Noe, F.1    Horenko, I.2    Schutte, C.3    Smith, J.C.4
  • 42
    • 34249813736 scopus 로고    scopus 로고
    • Structural and pathway complexity of beta-strand reorganization within aggregates of human transthyretin(105-115) peptide
    • Li, D. W.; Han, L.; Huo, S. Structural and pathway complexity of beta-strand reorganization within aggregates of human transthyretin(105-115) peptide. J. Phys. Chem. B 2007, 111, 5425-5433.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 5425-5433
    • Li, D.W.1    Han, L.2    Huo, S.3
  • 43
    • 34248355596 scopus 로고    scopus 로고
    • The sequence TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase displays structural ambivalence and interconverts between alpha-helical and beta-hairpin conformations mediated by collapsed conformational states
    • Patel, S.; Balaji, P. V.; Sasidhar, Y. U. The sequence TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase displays structural ambivalence and interconverts between alpha-helical and beta-hairpin conformations mediated by collapsed conformational states. J. Pept. Sci. 2007, 13, 314-326.
    • (2007) J. Pept. Sci , vol.13 , pp. 314-326
    • Patel, S.1    Balaji, P.V.2    Sasidhar, Y.U.3
  • 44
    • 34247520870 scopus 로고    scopus 로고
    • Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation
    • Roccatano, D.; Barthel, A.; Zacharias, M. Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation. Biopolymers 2007, 85, 407-421.
    • (2007) Biopolymers , vol.85 , pp. 407-421
    • Roccatano, D.1    Barthel, A.2    Zacharias, M.3
  • 45
    • 34247868242 scopus 로고    scopus 로고
    • The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis
    • Sefcikova, J.; Krasovska, M. V.; Sponer, J.; Walter, N. G. The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis. Nucl. Acids Res. 2007, 35, 1933-1946.
    • (2007) Nucl. Acids Res , vol.35 , pp. 1933-1946
    • Sefcikova, J.1    Krasovska, M.V.2    Sponer, J.3    Walter, N.G.4
  • 46
    • 33646357500 scopus 로고    scopus 로고
    • RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics
    • Razga, F.; Zacharias, M.; Reblova, K.; Koca, J.; Sponer, J. RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics. Structure 2006, 14, 825-835.
    • (2006) Structure , vol.14 , pp. 825-835
    • Razga, F.1    Zacharias, M.2    Reblova, K.3    Koca, J.4    Sponer, J.5
  • 47
    • 33847178767 scopus 로고    scopus 로고
    • A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations
    • Kormos, B. L.; Baranger, A. M.; Beveridge, D. L. A study of collective atomic fluctuations and cooperativity in the U1A-RNA complex based on molecular dynamics simulations. J. Struct. Biol. 2007, 157, 500-513.
    • (2007) J. Struct. Biol , vol.157 , pp. 500-513
    • Kormos, B.L.1    Baranger, A.M.2    Beveridge, D.L.3
  • 48
    • 0027393187 scopus 로고
    • Statistical clustering techniques for the analysis of long molecular dynamics trajectories: Analysis of a 2.2-ns trajectories of YPGDV
    • Karpen, M. E.; Tobias, D. J.; Brooks, C. L., III Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of a 2.2-ns trajectories of YPGDV. Biochemistry 1993, 32, 412-420.
    • (1993) Biochemistry , vol.32 , pp. 412-420
    • Karpen, M.E.1    Tobias, D.J.2    Brooks III, C.L.3
  • 49
    • 84986532529 scopus 로고
    • Cluster analysis of molecular conformations
    • Shenkin, P. S.; McDonald, D. Q. Cluster analysis of molecular conformations. J. Comput. Chem. 1994, 15, 899-916.
    • (1994) J. Comput. Chem , vol.15 , pp. 899-916
    • Shenkin, P.S.1    McDonald, D.Q.2
  • 50
    • 0000490505 scopus 로고
    • A review of classification
    • Cormack, R. M. A review of classification. J. R. Stat. Soc. A 1971, 134, 321-367.
    • (1971) J. R. Stat. Soc. A , vol.134 , pp. 321-367
    • Cormack, R.M.1
  • 52
    • 84986435778 scopus 로고
    • Algorithms for clustering molecular dynamics configurations
    • Torda, A. E.; van Gunsteren, W. F. Algorithms for clustering molecular dynamics configurations. J. Comput. Chem. 1994, 15, 1331-1340.
    • (1994) J. Comput. Chem , vol.15 , pp. 1331-1340
    • Torda, A.E.1    van Gunsteren, W.F.2
  • 53
    • 0020537691 scopus 로고
    • Models for the conformational behaviour of angiotensin-II in acidic aqueous solutions
    • Marchionini, C.; Maigret, B.; Premilat, S. Models for the conformational behaviour of angiotensin-II in acidic aqueous solutions. Biochem. Biophys. Res. Comm. 1983, 112, 339-346.
    • (1983) Biochem. Biophys. Res. Comm , vol.112 , pp. 339-346
    • Marchionini, C.1    Maigret, B.2    Premilat, S.3
  • 55
    • 0024632867 scopus 로고
    • Computer simulation of the conformational behavior of cholecystokinin fragments: Conformational families of sulfated CCK8
    • Kreissler, M.; Pesquer, M.; Maigret, B.; Fournie-Zaluski, M. C.; Roques, B. P. Computer simulation of the conformational behavior of cholecystokinin fragments: Conformational families of sulfated CCK8. J. Comput.-Aided Mol. Des. 1989, 3, 85-94.
    • (1989) J. Comput.-Aided Mol. Des , vol.3 , pp. 85-94
    • Kreissler, M.1    Pesquer, M.2    Maigret, B.3    Fournie-Zaluski, M.C.4    Roques, B.P.5
  • 56
    • 0024395940 scopus 로고
    • A 3D building blocks approach to analyzing and predicting structure of proteins
    • Unger, R.; Harel, D.; Wherland, S.; Sussman, J. L. A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins 1989, 5, 355-373.
    • (1989) Proteins , vol.5 , pp. 355-373
    • Unger, R.1    Harel, D.2    Wherland, S.3    Sussman, J.L.4
  • 57
    • 0026665439 scopus 로고
    • Fuzzy cluster analysis of molecular dynamics trajectories
    • Gordon, H. L.; Somorjai, R. L. Fuzzy cluster analysis of molecular dynamics trajectories. Proteins 1992, 14, 249-264.
    • (1992) Proteins , vol.14 , pp. 249-264
    • Gordon, H.L.1    Somorjai, R.L.2
  • 58
    • 1842308698 scopus 로고
    • Multiconformational, investigations of polypeptidic structures, using clustering methods and principal component analysis
    • Michel, A.; Jeandenans, C. Multiconformational, investigations of polypeptidic structures, using clustering methods and principal component analysis. Comput. Chem. 1993, 17, 49-59.
    • (1993) Comput. Chem , vol.17 , pp. 49-59
    • Michel, A.1    Jeandenans, C.2
  • 59
    • 0029152775 scopus 로고
    • Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory
    • Troyer, J. M.; Cohen, F. E. Protein conformational landscapes: energy minimization and clustering of a long molecular dynamics trajectory. Proteins 1995, 23, 97-110.
    • (1995) Proteins , vol.23 , pp. 97-110
    • Troyer, J.M.1    Cohen, F.E.2
  • 60
    • 0033557181 scopus 로고    scopus 로고
    • Folding-unfolding thermodynamics of a b-heptapeptide from equilibrium simulations
    • Daura, X.; van Gunsteren, W. F.; Mark, A. E. Folding-unfolding thermodynamics of a b-heptapeptide from equilibrium simulations. Proteins 1999, 34, 269-280.
    • (1999) Proteins , vol.34 , pp. 269-280
    • Daura, X.1    van Gunsteren, W.F.2    Mark, A.E.3
  • 61
    • 0034275729 scopus 로고    scopus 로고
    • Clustering of a molecular dynamics trajectory with a Hamming distance
    • Gabarro-Arpa, J.; Revilla, R. Clustering of a molecular dynamics trajectory with a Hamming distance. Comput. Chem. 2000, 24, 696-698.
    • (2000) Comput. Chem , vol.24 , pp. 696-698
    • Gabarro-Arpa, J.1    Revilla, R.2
  • 62
    • 0035028483 scopus 로고    scopus 로고
    • Conformational space comparison of GnRH and 1GnRH-III using molecular dynamics, cluster analysis and Monte Carlo thermodynamic integration
    • Watts, C. R.; Mezei, M.; Murphy, R. F.; Lovas, S. Conformational space comparison of GnRH and 1GnRH-III using molecular dynamics, cluster analysis and Monte Carlo thermodynamic integration. J. Biomol. Struct. Dyn. 2001, 18, 733-748.
    • (2001) J. Biomol. Struct. Dyn , vol.18 , pp. 733-748
    • Watts, C.R.1    Mezei, M.2    Murphy, R.F.3    Lovas, S.4
  • 63
    • 0036568284 scopus 로고    scopus 로고
    • Hamming distance geometry of a protein conformational space: Application, to the clustering of a 4-ns molecular dynamics trajectory of the HIV-1 integrase catalytic core
    • Laboulais, C.; Ouali, M.; Le Bret, M.; Gabarro-Arpa, J. Hamming distance geometry of a protein conformational space: Application, to the clustering of a 4-ns molecular dynamics trajectory of the HIV-1 integrase catalytic core. Proteins 2002, 47, 169-179.
    • (2002) Proteins , vol.47 , pp. 169-179
    • Laboulais, C.1    Ouali, M.2    Le Bret, M.3    Gabarro-Arpa, J.4
  • 64
    • 0037498095 scopus 로고    scopus 로고
    • Fuzzy clustering as a means of selecting representative conformers and molecular alignments
    • Feher, M.; Schmidt, J. M. Fuzzy clustering as a means of selecting representative conformers and molecular alignments. J. Chem. Inf. Comput. Sci. 2003, 43, 810-818.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 810-818
    • Feher, M.1    Schmidt, J.M.2
  • 65
    • 0037339393 scopus 로고    scopus 로고
    • Helix propensities of short peptides: Molecular, dynamics versus Bioinformatics
    • Bystroff, C.; Garde, S. Helix propensities of short peptides: Molecular, dynamics versus Bioinformatics. Proteins 2003, 50, 552-562.
    • (2003) Proteins , vol.50 , pp. 552-562
    • Bystroff, C.1    Garde, S.2
  • 66
    • 0037381819 scopus 로고    scopus 로고
    • Simulations of human lysozyme: Probing, the conformations triggering amyloidosis
    • Moraitakis, G.; Goodfellow, J. M. Simulations of human lysozyme: Probing, the conformations triggering amyloidosis. Biophys. J. 2003, 84, 2149-2158.
    • (2003) Biophys. J , vol.84 , pp. 2149-2158
    • Moraitakis, G.1    Goodfellow, J.M.2
  • 67
    • 17844406393 scopus 로고    scopus 로고
    • Large-scale conformational dynamics of the HTV-1 integrase core domain and its catalytic loop mutants
    • Lee, M. C.; Deng, J.; Briggs, J. M.; Duan, Y. Large-scale conformational dynamics of the HTV-1 integrase core domain and its catalytic loop mutants. Biophys. J. 2005, 88, 3133-3146.
    • (2005) Biophys. J , vol.88 , pp. 3133-3146
    • Lee, M.C.1    Deng, J.2    Briggs, J.M.3    Duan, Y.4
  • 68
    • 34548098593 scopus 로고    scopus 로고
    • Estimation of protein folding probability from equilibrium simulations
    • Rao, F.; Settanni, G.; Guarnera, E.; Caflisch, A. Estimation of protein folding probability from equilibrium simulations. J. Chem. Phys. 2005, 122, 184901.
    • (2005) J. Chem. Phys , vol.122 , pp. 184901
    • Rao, F.1    Settanni, G.2    Guarnera, E.3    Caflisch, A.4
  • 69
    • 33745759471 scopus 로고    scopus 로고
    • Ensemble-based convergence analysis of biomolecular trajectories
    • Lyman, E.; Zuckerman, D. M. Ensemble-based convergence analysis of biomolecular trajectories. Biophys. J. 2006, 91, 164-172.
    • (2006) Biophys. J , vol.91 , pp. 164-172
    • Lyman, E.1    Zuckerman, D.M.2
  • 70
    • 33748527186 scopus 로고    scopus 로고
    • Quantifying polypeptide conformational space: Sensitivity to conformation and ensemble definition
    • Sullivan, D. C.; Lim, C. Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition. J. Phys. Chem. B 2006, 110, 16707-16717.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 16707-16717
    • Sullivan, D.C.1    Lim, C.2
  • 71
    • 33746878817 scopus 로고    scopus 로고
    • Bayesian model based clustering analysis: Application to a molecular dynamics trajectory of the HIV-1 integrase catalytic core
    • Li, Y. Bayesian model based clustering analysis: application to a molecular dynamics trajectory of the HIV-1 integrase catalytic core. J. Chem. Inf. Model. 2006, 46, 1742-1750.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 1742-1750
    • Li, Y.1
  • 72
    • 17444404720 scopus 로고    scopus 로고
    • Foldamer simulations: Novel, computational methods and applications to poly-phenylacetylene oligomers
    • Elmer, S. P.; Pande, V. S. Foldamer simulations: Novel, computational methods and applications to poly-phenylacetylene oligomers. J. Chem. Phys. 2004, 121, 12760-12771.
    • (2004) J. Chem. Phys , vol.121 , pp. 12760-12771
    • Elmer, S.P.1    Pande, V.S.2
  • 73
    • 20544435097 scopus 로고    scopus 로고
    • Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
    • Sorin, E. J.; Pande, V. S. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys. J. 2005, 88, 2472-2493.
    • (2005) Biophys. J , vol.88 , pp. 2472-2493
    • Sorin, E.J.1    Pande, V.S.2
  • 74
    • 14744268628 scopus 로고    scopus 로고
    • Protein conformational space in higher order phi-psi maps
    • Sims, G. E.; Choi, I.-G.; Kim, S.-H. Protein conformational space in higher order phi-psi maps. Proc. Natl. Acad. Sci. 2005, 102, 618-621.
    • (2005) Proc. Natl. Acad. Sci , vol.102 , pp. 618-621
    • Sims, G.E.1    Choi, I.-G.2    Kim, S.-H.3
  • 75
    • 33646947896 scopus 로고    scopus 로고
    • Folding free-energy landscape of a 10-residue mini-protein, chignolin
    • Satoh, D.; Shimizu, K.; Nakamura, S.; Terada, T. Folding free-energy landscape of a 10-residue mini-protein, chignolin. FEES Lett. 2006, 580, 3422-3426.
    • (2006) FEES Lett , vol.580 , pp. 3422-3426
    • Satoh, D.1    Shimizu, K.2    Nakamura, S.3    Terada, T.4
  • 77
    • 0026699291 scopus 로고
    • Conformational substates in B-DNA
    • Poncin, M.; Hartmann, B.; Lavery, R. Conformational substates in B-DNA. J. Mol. Blol. 1992, 226, 775-794.
    • (1992) J. Mol. Blol , vol.226 , pp. 775-794
    • Poncin, M.1    Hartmann, B.2    Lavery, R.3
  • 78
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA and phosphoramidate helices
    • Srinivasan, J.; Cheatham, T. E., III; Cieplak, P.; Kollman, P. A.; Case, D. A. Continuum solvent studies of the stability of DNA, RNA and phosphoramidate helices. J. Am. Chem. Soc. 1998, 120, 9401-9409.
    • (1998) J. Am. Chem. Soc , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham III, T.E.2    Cieplak, P.3    Kollman, P.A.4    Case, D.A.5
  • 79
    • 0001351515 scopus 로고
    • Estimation of absolute and relative entropies of macromolecules using the covariance matrix
    • Schlitter, J. Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chem. Phys. Lett. 1993, 215, 617-621.
    • (1993) Chem. Phys. Lett , vol.215 , pp. 617-621
    • Schlitter, J.1
  • 82
    • 0343442766 scopus 로고
    • Knowledge acquisition via incremental conceptual clustering
    • Fisher, D. Knowledge acquisition via incremental conceptual clustering. Machine Learning 1987, 2, 139-172.
    • (1987) Machine Learning , vol.2 , pp. 139-172
    • Fisher, D.1
  • 83
    • 0002607026 scopus 로고    scopus 로고
    • Bayesian classification (Auto-Class): Theory and results
    • Fayyad, U. M, Piatetsky-Shapiro, G, Smyth, P, Uthurusamy, R, Eds, American Association of Artificial Intelligence Press: Menlo Park, CA
    • Cheeseman, P.; Stutz, J. Bayesian classification (Auto-Class): theory and results. In Advances in knowledge discovery and data mining; Fayyad, U. M., Piatetsky-Shapiro, G., Smyth, P., Uthurusamy, R., Eds.; American Association of Artificial Intelligence Press: Menlo Park, CA, 1996; pp 61-83.
    • (1996) Advances in knowledge discovery and data mining , pp. 61-83
    • Cheeseman, P.1    Stutz, J.2
  • 84
    • 0003263256 scopus 로고    scopus 로고
    • 3rd ed, Springer: Berlin-Heidelberg
    • Kohonen, T. Self-organizing maps, 3rd ed.; Springer: Berlin-Heidelberg, 2001; Vol. 30, p 501.
    • (2001) Self-organizing maps , vol.30 , pp. 501
    • Kohonen, T.1
  • 85
    • 0029633186 scopus 로고    scopus 로고
    • Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; Debolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structure and energetic properties of molecules. Comp. Phys. Comm. 1995, 91, 1-41.
    • Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; Debolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structure and energetic properties of molecules. Comp. Phys. Comm. 1995, 91, 1-41.
  • 86
    • 23444454552 scopus 로고    scopus 로고
    • Case, D. A.; Cheatham, T. E., III; Darden, T. A.; Gohlker, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A. V.; Simmerling, C.; Wang, B.; Woods, R. The AMBER biomolecular simulation programs. J. Comput. Chem. 2005, 26, 1668-1688.
    • Case, D. A.; Cheatham, T. E., III; Darden, T. A.; Gohlker, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A. V.; Simmerling, C.; Wang, B.; Woods, R. The AMBER biomolecular simulation programs. J. Comput. Chem. 2005, 26, 1668-1688.
  • 93
    • 33745184704 scopus 로고    scopus 로고
    • Biological cluster validity indices based on the gene ontology
    • Famili, A. F, Kok, J. N, Pena, J. M, Siebes, A, Feelders, A, Eds, Springer: Berlin, Heidelberg
    • Speer, N.; Spiet, C.; Zell, A. Biological cluster validity indices based on the gene ontology. In Advances in intelligent data analysis VI; Famili, A. F., Kok, J. N., Pena, J. M., Siebes, A., Feelders, A., Eds.; Springer: Berlin, Heidelberg, 2005; Vol. 3646, pp 429-439.
    • (2005) Advances in intelligent data analysis VI , vol.3646 , pp. 429-439
    • Speer, N.1    Spiet, C.2    Zell, A.3
  • 94
    • 84972893020 scopus 로고
    • A dendrite method for cluster analysis
    • Calinski, T.; Harabasz, J. A dendrite method for cluster analysis. Comm. Stat. 1974, 3, 1-27.
    • (1974) Comm. Stat , vol.3 , pp. 1-27
    • Calinski, T.1    Harabasz, J.2
  • 96
    • 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. Comp. Phys. 1977, 23, 327-341.
    • (1977) J. Comp. Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 98
    • 0029011701 scopus 로고    scopus 로고
    • Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
    • Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
  • 100
    • 0344796204 scopus 로고
    • Ion-water interaction potentials derived from free energy perturbation simulations
    • Aqvist, J. Ion-water interaction potentials derived from free energy perturbation simulations. J. Phys. Chem. 1990, 94, 8021-8024.
    • (1990) J. Phys. Chem , vol.94 , pp. 8021-8024
    • Aqvist, J.1
  • 101
    • 0031788539 scopus 로고    scopus 로고
    • Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution
    • Cheatham, T. E., III; Srinivasan, J.; Case, D. A.; Kollman, P. A. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J. Biomol. Struct. Dyn. 1998, 16, 265-280.
    • (1998) J. Biomol. Struct. Dyn , vol.16 , pp. 265-280
    • Cheatham III, T.E.1    Srinivasan, J.2    Case, D.A.3    Kollman, P.A.4
  • 102
    • 0000515108 scopus 로고    scopus 로고
    • Self-guided molecular dynamics simulation for efficient conformational search
    • Wu, X. W.; Wang, S. M. Self-guided molecular dynamics simulation for efficient conformational search. J. Phys. Chem. 1998, 102, 7238-7250.
    • (1998) J. Phys. Chem , vol.102 , pp. 7238-7250
    • Wu, X.W.1    Wang, S.M.2
  • 103
    • 0035932703 scopus 로고    scopus 로고
    • Helix Folding of an Alanine-Based Peptide in Explicit Water
    • Wu, X.; Wang, S. Helix Folding of an Alanine-Based Peptide in Explicit Water. J. Phys. Chem. B 2001, 105, 2227-2235.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 2227-2235
    • Wu, X.1    Wang, S.2
  • 104
    • 1942519803 scopus 로고    scopus 로고
    • Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water
    • Wu, X.; Brooks, B. R. Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water. Biophys. J. 2004, 86, 1946-1958.
    • (2004) Biophys. J , vol.86 , pp. 1946-1958
    • Wu, X.1    Brooks, B.R.2
  • 105
    • 0037093874 scopus 로고    scopus 로고
    • Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation
    • Wu, X.; Wang, S.; Brooks, B. R. Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation. J. Am. Chem. Soc. 2002, 124, 5282-5283.
    • (2002) J. Am. Chem. Soc , vol.124 , pp. 5282-5283
    • Wu, X.1    Wang, S.2    Brooks, B.R.3
  • 108
    • 0032517340 scopus 로고    scopus 로고
    • Nucleic acid interactions of unfused aromatic cations: Evaluation of proposed minor-groove, major-groove, and intercalation binding modes
    • Wilson, W. D.; Tanious, F. A.; Ding, D.; Kumar, A.; Boykin, D. W.; Colson, P.; Houssier, C.; Bailly, C Nucleic acid interactions of unfused aromatic cations: Evaluation of proposed minor-groove, major-groove, and intercalation binding modes. J. Am. Chem. Soc. 1998, 120, 10310-10321.
    • (1998) J. Am. Chem. Soc , vol.120 , pp. 10310-10321
    • Wilson, W.D.1    Tanious, F.A.2    Ding, D.3    Kumar, A.4    Boykin, D.W.5    Colson, P.6    Houssier, C.7    Bailly, C.8
  • 110
    • 0002636134 scopus 로고
    • Pairwise solute descreening of solute charges from a dielectric medium
    • Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Pairwise solute descreening of solute charges from a dielectric medium. Chem. Phys. Lett. 1995, 246, 122-129.
    • (1995) Chem. Phys. Lett , vol.246 , pp. 122-129
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 111
    • 0034701222 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acids with a generalized Born solvation model
    • Tsui, V.; Case, D. A. Molecular dynamics simulations of nucleic acids with a generalized Born solvation model. J. Am. Chem. Soc. 2000, 122, 2489-2498.
    • (2000) J. Am. Chem. Soc , vol.122 , pp. 2489-2498
    • Tsui, V.1    Case, D.A.2
  • 112
    • 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. Graphics Modell. 2006, 25, 247-260.
    • (2006) J. Mol. Graphics Modell , vol.25 , pp. 247-260
    • Wang, J.1    Wang, W.2    Kollman, P.A.3    Case, D.A.4
  • 113
    • 0035451865 scopus 로고    scopus 로고
    • Automatic parameterization of force field by systematic search and genetic algorithms
    • Wang, J.; Kollman, P. A. Automatic parameterization of force field by systematic search and genetic algorithms. J. Comput. Chem. 2001, 22, 1219-1228.
    • (2001) J. Comput. Chem , vol.22 , pp. 1219-1228
    • Wang, J.1    Kollman, P.A.2
  • 114
    • 3042524904 scopus 로고    scopus 로고
    • Bayly, C. I.; Cieplak, P.; Cornell, W. D.; 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.
    • Bayly, C. I.; Cieplak, P.; Cornell, W. D.; 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.
  • 115
    • 36649004673 scopus 로고    scopus 로고
    • Frisch, M. J, Trucks, G. W, Schlegel, H. B, Scuseria, G. E, Robb, M. A, J. R. Cheeseman, V. G. Z, Montgomery, J. A, Jr, Stratmann, R. E, Burant, J. C, Dapprich, S, Millam, J. M, Daniels, A. D, Kudin, K. N, Strain, M. C, Farkas, O, Tomasi, J, Barone, V, Cossi, M, Cammi, R, Mennucci, B, Pomelli, C, Adamo, C, Clifford, S, Ochterski, J, Petersson, G. A, Ayala, P. Y, Cui, Q, Morokuma, K, Salvador, P, Dannenberg, J. J, Malick, D. K, Rabuck, A. D, Raghavachari, K, Foresman, J. B, Cioslowski, J, Ortiz, J. V, Baboul, A. G, Stefanov, B. B, Liu, G, Liashenko, A, Piskorz, P, Komaromi, I, Gomperts, R, Martin, R. L, Fox, D. J, Keith, T, Al-Laham, M. A, Peng, C. Y, Nanayakkara, A, Challacombe, M, Gill, P. M. W, Johnson, B, Chen, W, Wong, M. W, Andres, J. L, Gonzalez, C, Head-Gordon, M, Replogle, E. S, Pople, J. A. Gaussian 98 Revision A. 10, Gaussian, Inc, Pittsburgh, PA, 2001
    • Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; J. R. Cheeseman, V. G. Z.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Salvador, P.; Dannenberg, J. J.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98 (Revision A. 10); Gaussian, Inc.: Pittsburgh, PA, 2001.
  • 116
    • 0029928846 scopus 로고    scopus 로고
    • A crystallographic and spectroscopic study of the complex between d(CGCGAAT-TCGCG)2 and 2,5-bis(4-guanylphenyl)furan, an analogue of Berenil: Structural origins of enhanced DNA-binding affinity
    • Laughton, C. A.; Tanious, F. A.; Nunn, C. M.; Boykin, D. W.; Wilson, W. D.; Neidle, S. A crystallographic and spectroscopic study of the complex between d(CGCGAAT-TCGCG)2 and 2,5-bis(4-guanylphenyl)furan, an analogue of Berenil: structural origins of enhanced DNA-binding affinity. Biochemistry 1996, 35, 5655-5661.
    • (1996) Biochemistry , vol.35 , pp. 5655-5661
    • Laughton, C.A.1    Tanious, F.A.2    Nunn, C.M.3    Boykin, D.W.4    Wilson, W.D.5    Neidle, S.6


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