메뉴 건너뛰기




Volumn 6, Issue 7, 2010, Pages 5-

Mechanism of microRNA-target interaction: Molecular dynamics simulations and thermodynamics analysis

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CATALYST ACTIVITY; METAL IONS; METALS; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; SUBSTRATES; THERMOANALYSIS; THERMODYNAMIC PROPERTIES;

EID: 78049314237     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000866     Document Type: Article
Times cited : (75)

References (72)
  • 1
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 2
    • 37648998629 scopus 로고    scopus 로고
    • Getting to the root of miRNAmediated gene silencing
    • Eulalio A, Huntzinger E, Izaurralde E (2008) Getting to the root of miRNAmediated gene silencing. Cell 132: 9-14.
    • (2008) Cell , vol.132 , pp. 9-14
    • Eulalio, A.1    Huntzinger, E.2    Izaurralde, E.3
  • 3
    • 33748928159 scopus 로고    scopus 로고
    • The diverse functions of microRNAs in animal development and disease
    • Kloosterman WP, Plasterk RHA (2006) The diverse functions of microRNAs in animal development and disease. Dev Cell 11: 441-450.
    • (2006) Dev Cell , vol.11 , pp. 441-450
    • Kloosterman, W.P.1    Plasterk, R.H.A.2
  • 4
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120(1): 15-20.
    • (2005) Cell , vol.120 , Issue.1 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 5
    • 0038299558 scopus 로고    scopus 로고
    • Role of microRNAs in plant and animal development
    • Carrington JC, Ambros V (2003) Role of microRNAs in plant and animal development. Science 301: 336-338.
    • (2003) Science , vol.301 , pp. 336-338
    • Carrington, J.C.1    Ambros, V.2
  • 6
    • 0034708122 scopus 로고    scopus 로고
    • The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
    • Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403(6772): 901-906.
    • (2000) Nature , vol.403 , Issue.6772 , pp. 901-906
    • Reinhart, B.J.1    Slack, F.J.2    Basson, M.3    Pasquinelli, A.E.4    Bettinger, J.C.5
  • 8
    • 33748587841 scopus 로고    scopus 로고
    • A patternbased method for the identification of MicroRNA binding sites and their corresponding heteroduplexes
    • Miranda KC, Huynh T, Tay Y, Ang Y-S, Tam W-L, et al. (2006) A patternbased method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126(6): 1203-1217.
    • (2006) Cell , vol.126 , Issue.6 , pp. 1203-1217
    • Miranda, K.C.1    Huynh, T.2    Tay, Y.3    Ang, Y.-S.4    Tam, W.-L.5
  • 9
    • 34250832061 scopus 로고    scopus 로고
    • Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319
    • Palatnik JF, Wollmann H, Schommer C, Schwab R, Boisbouvier J, et al. (2007) Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev Cell 13(1): 115-125.
    • (2007) Dev Cell , vol.13 , Issue.1 , pp. 115-125
    • Palatnik, J.F.1    Wollmann, H.2    Schommer, C.3    Schwab, R.4    Boisbouvier, J.5
  • 10
    • 2942672580 scopus 로고    scopus 로고
    • Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    • Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14(6): 787-799.
    • (2004) Mol Cell , vol.14 , Issue.6 , pp. 787-799
    • Jones-Rhoades, M.W.1    Bartel, D.P.2
  • 11
    • 58849093262 scopus 로고    scopus 로고
    • Revisiting the principles of microRNA target recognition and mode of action
    • Brodersen P, Voinnet O (2009) Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol 10(2): 141-148.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , Issue.2 , pp. 141-148
    • Brodersen, P.1    Voinnet, O.2
  • 12
    • 4444302947 scopus 로고    scopus 로고
    • Crystal structure of Argonaute and its implications for RISC slicer activity
    • Song JJ, Smith SK, Hannon GJ, Joshua-Tor L (2004) Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305: 1434-1437.
    • (2004) Science , vol.305 , pp. 1434-1437
    • Song, J.J.1    Smith, S.K.2    Hannon, G.J.3    Joshua-Tor, L.4
  • 14
    • 11244279683 scopus 로고    scopus 로고
    • Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity
    • Parker JS, Roe S, Barford D (2004) Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J 23: 4727-4737.
    • (2004) EMBO J , vol.23 , pp. 4727-4737
    • Parker, J.S.1    Roe, S.2    Barford, D.3
  • 15
    • 0034306266 scopus 로고    scopus 로고
    • Domains in gene silencing and cell differentiation proteins: The novel PAZ domain and redefinition of the Piwi domain
    • Cerutti L, Mian N, Bateman A (2000) Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain. Trends Biochem Sci 25(10): 481-482.
    • (2000) Trends Biochem Sci , vol.25 , Issue.10 , pp. 481-482
    • Cerutti, L.1    Mian, N.2    Bateman, A.3
  • 17
    • 32344448109 scopus 로고    scopus 로고
    • Argonaute and RNA-getting into the groove
    • Song JJ, Joshua-Tor L (2006) Argonaute and RNA-getting into the groove. Curr Opin Struct Biol 16(1): 5-11.
    • (2006) Curr Opin Struct Biol , vol.16 , Issue.1 , pp. 5-11
    • Song, J.J.1    Joshua-Tor, L.2
  • 18
    • 0029643952 scopus 로고
    • Recombining the structures of HIV integrase, RuvC and RNase H
    • Yang W, Steitz TA (1995) Recombining the structures of HIV integrase, RuvC and RNase H. Structure 3: 131-134.
    • (1995) Structure , vol.3 , pp. 131-134
    • Yang, W.1    Steitz, T.A.2
  • 20
    • 57749206034 scopus 로고    scopus 로고
    • Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
    • Wang Y, Juranek S, Li H, Sheng G, Tuschl T, et al. (2008) Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456: 921-926.
    • (2008) Nature , vol.456 , pp. 921-926
    • Wang, Y.1    Juranek, S.2    Li, H.3    Sheng, G.4    Tuschl, T.5
  • 21
    • 70349961432 scopus 로고    scopus 로고
    • Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes
    • Wang Y, Juranek S, Li H, Sheng G, Wardle GS, et al. (2009) Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461(7265): 754-761.
    • (2009) Nature , vol.461 , Issue.7265 , pp. 754-761
    • Wang, Y.1    Juranek, S.2    Li, H.3    Sheng, G.4    Wardle, G.S.5
  • 22
    • 2342626647 scopus 로고    scopus 로고
    • The RNA-induced silencing complex is a Mg21-dependent endonuclease
    • Schwarz DS, Tomari Y, Zamore PD (2004) The RNA-induced silencing complex is a Mg21-dependent endonuclease. Curr Biol 14: 787-791.
    • (2004) Curr Biol , vol.14 , pp. 787-791
    • Schwarz, D.S.1    Tomari, Y.2    Zamore, P.D.3
  • 23
    • 0035863097 scopus 로고    scopus 로고
    • RNA interference is mediated by 21- and 22-nucleotide RNAs
    • Elbashir SM, Lendeckel W, Tuschl T (2001) RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev 15: 188-200.
    • (2001) Genes Dev , vol.15 , pp. 188-200
    • Elbashir, S.M.1    Lendeckel, W.2    Tuschl, T.3
  • 24
    • 0035803583 scopus 로고    scopus 로고
    • Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate
    • Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T (2001) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 20: 6877-6888.
    • (2001) EMBO J , vol.20 , pp. 6877-6888
    • Elbashir, S.M.1    Martinez, J.2    Patkaniowska, A.3    Lendeckel, W.4    Tuschl, T.5
  • 25
    • 0033955909 scopus 로고    scopus 로고
    • Protein thermal stability: Insights from atomic displacement parameters (B values)
    • Parthasarathy S, Murthy MRN (2000) Protein thermal stability: insights from atomic displacement parameters (B values). Protein Eng 13(1): 9-13.
    • (2000) Protein Eng , vol.13 , Issue.1 , pp. 9-13
    • Parthasarathy, S.1    Murthy, M.R.N.2
  • 29
    • 0036888353 scopus 로고    scopus 로고
    • Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50
    • Hayward S, Lee RA (2002) Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J Mol Graph Model 21: 181-183.
    • (2002) J Mol Graph Model , vol.21 , pp. 181-183
    • Hayward, S.1    Lee, R.A.2
  • 30
    • 0030883755 scopus 로고    scopus 로고
    • Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates
    • Wriggers W, Schulten K (1997) Protein domain movements: Detection of rigid domains and visualization of hinges in comparisons of atomic coordinates. Proteins 29: 1-14.
    • (1997) Proteins , vol.29 , pp. 1-14
    • Wriggers, W.1    Schulten, K.2
  • 31
    • 56249145105 scopus 로고    scopus 로고
    • Structure of the guide- strand- containing Argonaute silencing complex
    • Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ (2008) Structure of the guide- strand- containing Argonaute silencing complex. Nature 456(7219): 209-213.
    • (2008) Nature , vol.456 , Issue.7219 , pp. 209-213
    • Wang, Y.1    Sheng, G.2    Juranek, S.3    Tuschl, T.4    Patel, D.J.5
  • 32
    • 34250805982 scopus 로고    scopus 로고
    • MicroRNA targeting specificity in mammals: Determinants beyond seed pairing
    • Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27(1): 91-105.
    • (2007) Mol Cell , vol.27 , Issue.1 , pp. 91-105
    • Grimson, A.1    Farh, K.K.2    Johnston, W.K.3    Garrett-Engele, P.4    Lim, L.P.5
  • 34
    • 2442495329 scopus 로고    scopus 로고
    • RISC is 59 phospomonoester producing RNA endonulease
    • Martinez J, Tuschl T (2004) RISC is 59 phospomonoester producing RNA endonulease. Genes Dev 18: 975-980.
    • (2004) Genes Dev , vol.18 , pp. 975-980
    • Martinez, J.1    Tuschl, T.2
  • 36
    • 33750997616 scopus 로고    scopus 로고
    • Protein-RNA interactions: Exploring binding patters with a three-dimensional superposition analysis of high resolution structures
    • Morozova N, Allers J, Myers J, Shamoo Y (2006) Protein-RNA interactions: exploring binding patters with a three-dimensional superposition analysis of high resolution structures. Bioinformatics 22(22): 2746-2752.
    • (2006) Bioinformatics , vol.22 , Issue.22 , pp. 2746-2752
    • Morozova, N.1    Allers, J.2    Myers, J.3    Shamoo, Y.4
  • 37
    • 0035892161 scopus 로고    scopus 로고
    • Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics
    • Tsui V, Case DA (2001) Calculations of the absolute free energies of binding between RNA and metal ions using molecular dynamics simulations and continuum electrostatics. J Phys Chem B 105: 11314-11325.
    • (2001) J Phys Chem B , vol.105 , pp. 11314-11325
    • Tsui, V.1    Case, D.A.2
  • 38
    • 58649113420 scopus 로고    scopus 로고
    • Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein
    • Parker JS, Parizotto EA, Wang M, Roe SM, Barford D (2009) Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Mol Cell 33(2): 204-214.
    • (2009) Mol Cell , vol.33 , Issue.2 , pp. 204-214
    • Parker, J.S.1    Parizotto, E.A.2    Wang, M.3    Roe, S.M.4    Barford, D.5
  • 39
    • 0347985826 scopus 로고    scopus 로고
    • Size selective recognition of siRNA by an RNA silencing suppressor
    • Vargason JM, Szittya G, Burgyan J, Hall TMT (2003) Size selective recognition of siRNA by an RNA silencing suppressor. Cell 115(7): 799-811.
    • (2003) Cell , vol.115 , Issue.7 , pp. 799-811
    • Vargason, J.M.1    Szittya, G.2    Burgyan, J.3    Hall, T.M.T.4
  • 40
    • 0030728865 scopus 로고    scopus 로고
    • Molecular dynamics of acetylcholinesterase dimer complexed with tacrine
    • Wlodek ST, Clark TW, Scott LR, McCammon JA (1997) Molecular dynamics of acetylcholinesterase dimer complexed with tacrine. J Am Chem Soc 119(40): 9513-9522.
    • (1997) J Am Chem Soc , vol.119 , Issue.40 , pp. 9513-9522
    • Wlodek, S.T.1    Clark, T.W.2    Scott, L.R.3    McCammon, J.A.4
  • 42
    • 29144505309 scopus 로고    scopus 로고
    • The widespread impact of mammalian microRNAs on mRNA repression and evolution
    • Farh KK (2005) The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310: 1817-1821.
    • (2005) Science , vol.310 , pp. 1817-1821
    • Farh, K.K.1
  • 43
    • 77951133902 scopus 로고    scopus 로고
    • Energetic decomposition with the Generalized-Born and Poisson-Boltzmann solvent models: Lessons from association of G-Protein components
    • Carrascal N, Green DF. Energetic decomposition with the Generalized-Born and Poisson-Boltzmann solvent models: Lessons from association of G-Protein components. J Phys Chem B 2010, 114: 5096-5116.
    • (2010) J Phys Chem B , vol.114 , pp. 5096-5116
    • Carrascal, N.1    Green, D.F.2
  • 44
    • 0642345790 scopus 로고    scopus 로고
    • Structure and conserved RNA binding of the PAZ domain
    • Yan KS, Yan S, Farooq A, Han A, Zeng L, et al. (2003) Structure and conserved RNA binding of the PAZ domain. Nature 426: 469-474.
    • (2003) Nature , vol.426 , pp. 469-474
    • Yan, K.S.1    Yan, S.2    Farooq, A.3    Han, A.4    Zeng, L.5
  • 45
    • 77249176042 scopus 로고    scopus 로고
    • Toward system level understanding of the miRNA pathway via mathematical modeling
    • Wang X, Li Y, Xu X, Wang Y-H (2010) Toward system level understanding of the miRNA pathway via mathematical modeling. Biosystem 100(1): 31-38.
    • (2010) Biosystem , vol.100 , Issue.1 , pp. 31-38
    • Wang, X.1    Li, Y.2    Xu, X.3    Wang, Y.-H.4
  • 46
    • 0345490960 scopus 로고    scopus 로고
    • The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes
    • Song JJ, Liu J, Tolia NH, Schneiderman J, Smith SK, et al. (2003) The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol 10(12): 1026-1032.
    • (2003) Nat Struct Biol , vol.10 , Issue.12 , pp. 1026-1032
    • Song, J.J.1    Liu, J.2    Tolia, N.H.3    Schneiderman, J.4    Smith, S.K.5
  • 47
    • 34447102459 scopus 로고    scopus 로고
    • Molecular basis for target RNA recognition and cleavage by human RISC
    • Ameres SL, Martinez J, Schroeder R (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130: 101-112.
    • (2007) Cell , vol.130 , pp. 101-112
    • Ameres, S.L.1    Martinez, J.2    Schroeder, R.3
  • 48
    • 0036544755 scopus 로고    scopus 로고
    • Micro RNAs are complementary to 30 UTR sequence motifs that mediate negative post-transcriptional regulation
    • Lai EC (2002) Micro RNAs are complementary to 30 UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 30: 363-364.
    • (2002) Nat Genet , vol.30 , pp. 363-364
    • Lai, E.C.1
  • 49
    • 33846614547 scopus 로고    scopus 로고
    • In silico selection of active siRNA
    • Patzel V (2007) In silico selection of active siRNA. Drug Discov Today 12(3-4): 139-148.
    • (2007) Drug Discov Today , vol.12 , Issue.3-4 , pp. 139-148
    • Patzel, V.1
  • 50
    • 42449094162 scopus 로고    scopus 로고
    • Solution structure of a let-7 miRNA: Lin-41 mRNA complex from C. elegans
    • Cevec M, Thibaudeau C, Plavec J (2008) Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans. Nucleic Acids Res 36(7): 2330-2337.
    • (2008) Nucleic Acids Res , vol.36 , Issue.7 , pp. 2330-2337
    • Cevec, M.1    Thibaudeau, C.2    Plavec, J.3
  • 51
    • 78049301652 scopus 로고    scopus 로고
    • 6.8 ed.; Tripos Inc.: St. Louis, MO
    • Tripos, 6.8 ed.; Tripos Inc.: St. Louis, MO, 2001.
    • (2001)
    • Tripos1
  • 52
    • 0034193510 scopus 로고    scopus 로고
    • Protein docking using spherical polar Fourier correlations
    • Ritchie DW, Kemp GJ (2000) Protein docking using spherical polar Fourier correlations. Proteins 39(2): 178-194.
    • (2000) Proteins , vol.39 , Issue.2 , pp. 178-194
    • Ritchie, D.W.1    Kemp, G.J.2
  • 53
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, et al. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19: 1639-1662.
    • (1998) J Comput Chem , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5
  • 54
    • 0037137609 scopus 로고    scopus 로고
    • AutoDocking dinucleotides to the HIV-1 integrase core domain: Exploring possible binding sites for viral and genomic DNA
    • Perryman AL, McCammon JA (2002) AutoDocking dinucleotides to the HIV-1 integrase core domain: exploring possible binding sites for viral and genomic DNA. J Med Chem 45(26): 624-5627.
    • (2002) J Med Chem , vol.45 , Issue.26 , pp. 624-5627
    • Perryman, A.L.1    McCammon, J.A.2
  • 55
    • 0029633168 scopus 로고
    • GROMACS: A message-passing parallel molecular dynamics implementation
    • Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS: A message-passing parallel molecular dynamics implementation. Comput Phys Commun 91(1-3): 43-56.
    • (1995) Comput Phys Commun , vol.91 , Issue.1-3 , pp. 43-56
    • Berendsen, H.J.C.1    van der Spoel, D.2    van Drunen, R.3
  • 56
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang J, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21: 1049-1074.
    • (2000) J Comput Chem , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 58
    • 33846086933 scopus 로고    scopus 로고
    • Canonical sampling through velocity rescaling
    • Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys 126(1): 14101-1-14101-7.
    • (2007) J Chem Phys , vol.126 , Issue.1 , pp. 141011-141017
    • Bussi, G.1    Donadio, D.2    Parrinello, M.3
  • 59
    • 33846823909 scopus 로고
    • Particle mesh Ewald; an nlog(n) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L (1993) Particle mesh Ewald; an nlog(n) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 61
    • 0030728865 scopus 로고    scopus 로고
    • Molecular dynamics of acetylcholinesterase dimer complexed with tacrine
    • Wlodek ST, Clark TW, Scott LR, McCammon JA (1997) Molecular dynamics of acetylcholinesterase dimer complexed with tacrine. J Am Chem Soc 119: 9513-9522.
    • (1997) J Am Chem Soc , vol.119 , pp. 9513-9522
    • Wlodek, S.T.1    Clark, T.W.2    Scott, L.R.3    McCammon, J.A.4
  • 62
    • 0033117937 scopus 로고    scopus 로고
    • Investigating protein dynamics in collective coordinate space
    • Kitao A, Go N (1999) Investigating protein dynamics in collective coordinate space. Curr Opin Struct Biol 9: 164-169.
    • (1999) Curr Opin Struct Biol , vol.9 , pp. 164-169
    • Kitao, A.1    Go, N.2
  • 63
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman P (1993) Free energy calculations: Applications to chemical and biochemical phenomena. Chem Rev 93: 2395-2417.
    • (1993) Chem Rev , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 64
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, et al. (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc Chem Res 33: 889-897.
    • (2000) Acc Chem Res , vol.33 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.5
  • 65
    • 0025283002 scopus 로고
    • Electrostatic interactions in macromolecules-theory and applications
    • Sharp KA, Honig B (1990) Electrostatic interactions in macromolecules-theory and applications. Annu Rev Biophys Biophys Chem 19: 301-332.
    • (1990) Annu Rev Biophys Biophys Chem , vol.19 , pp. 301-332
    • Sharp, K.A.1    Honig, B.2
  • 66
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • Sitkoff D, Sharp KA, Honig B (1994) Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 98: 1978-1988.
    • (1994) J Phys Chem , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 67
    • 0037442584 scopus 로고    scopus 로고
    • Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 49,6-diamidino-2-phenylindole and DNA duplexes in solution
    • Spackova N, Cheatham TE, Ryjacek F, Lankas F, van Meervelt L, et al. (2003) Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 49,6-diamidino-2-phenylindole and DNA duplexes in solution. J Am Chem Soc 125(7): 1759-1769.
    • (2003) J Am Chem Soc , vol.125 , Issue.7 , pp. 1759-1769
    • Spackova, N.1    Cheatham, T.E.2    Ryjacek, F.3    Lankas, F.4    van Meervelt, L.5
  • 68
    • 33750467966 scopus 로고    scopus 로고
    • Ligand affinities predicted with the MM/PBSA method: Dependence on the simulation method and the force field
    • Weis A, Katebzadeh K, Söderhjelm P, Nilsson I, Ryde U (2006) Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field. J Med Chem 49: 6596-6606.
    • (2006) J Med Chem , vol.49 , pp. 6596-6606
    • Weis, A.1    Katebzadeh, K.2    Söderhjelm, P.3    Nilsson, I.4    Ryde, U.5
  • 69
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • Sanner MF, Olson AJ, Spehner J-C (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38(3): 305-320.
    • (1996) Biopolymers , vol.38 , Issue.3 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.-C.3
  • 70
    • 84961980685 scopus 로고    scopus 로고
    • Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
    • Kuhn B, Kollman PA (2000) Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J Med Chem 43: 3786-3791.
    • (2000) J Med Chem , vol.43 , pp. 3786-3791
    • Kuhn, B.1    Kollman, P.A.2
  • 72
    • 1842479952 scopus 로고    scopus 로고
    • Exploring protein native states and large-scale conformational changes with a modified generalized born model
    • Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins Struct Funct Bioinf 55: 383-394.
    • (2004) Proteins Struct Funct Bioinf , vol.55 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.