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Volumn 10, Issue 3, 2014, Pages 1292-1301

Modified amber force field correctly models the conformational preference for tandem GA pairs in RNA

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EID: 84896292945     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct400861g     Document Type: Article
Times cited : (16)

References (65)
  • 1
    • 34547892624 scopus 로고    scopus 로고
    • A view of RNase P
    • Altman, S. A view of RNase P Mol. BioSyst. 2007, 3, 604-607
    • (2007) Mol. BioSyst. , vol.3 , pp. 604-607
    • Altman, S.1
  • 2
    • 0037062949 scopus 로고    scopus 로고
    • The chemical repertoire of natural ribozymes
    • Doudna, J. A.; Cech, T. R. The chemical repertoire of natural ribozymes Nature 2002, 418, 222-228
    • (2002) Nature , vol.418 , pp. 222-228
    • Doudna, J.A.1    Cech, T.R.2
  • 3
    • 0035656688 scopus 로고    scopus 로고
    • Noncoding RNA genes and the modern RNA world
    • Eddy, S. R. Noncoding RNA genes and the modern RNA world Nat. Rev. Genet. 2001, 2, 919-929
    • (2001) Nat. Rev. Genet. , vol.2 , pp. 919-929
    • Eddy, S.R.1
  • 4
    • 0034637161 scopus 로고    scopus 로고
    • The structural basis of ribosome activity in peptide bond synthesis
    • Nissen, P.; Hansen, J.; Ban, N.; Moore, P. B.; Steitz, T. A. The structural basis of ribosome activity in peptide bond synthesis Science 2000, 289, 920-930
    • (2000) Science , vol.289 , pp. 920-930
    • Nissen, P.1    Hansen, J.2    Ban, N.3    Moore, P.B.4    Steitz, T.A.5
  • 6
    • 38148999355 scopus 로고    scopus 로고
    • Let me count the ways: Mechanisms of gene regulation by miRNAs and siRNAs
    • Wu, L.; Belasco, J. G. Let me count the ways: Mechanisms of gene regulation by miRNAs and siRNAs Mol. Cell 2008, 29, 1-7
    • (2008) Mol. Cell , vol.29 , pp. 1-7
    • Wu, L.1    Belasco, J.G.2
  • 8
    • 34548778155 scopus 로고    scopus 로고
    • Ribozymes, riboswitches and beyond: Regulation of gene expression without proteins
    • Serganov, A.; Patel, D. J. Ribozymes, riboswitches and beyond: Regulation of gene expression without proteins Nat. Rev. Genet. 2007, 8, 776-790
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 776-790
    • Serganov, A.1    Patel, D.J.2
  • 9
    • 20444478991 scopus 로고    scopus 로고
    • Riboswitches as versatile gene control elements
    • Tucker, B. J.; Breaker, R. R. Riboswitches as versatile gene control elements Curr. Opin. Struct. Biol. 2005, 15, 342-348
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 342-348
    • Tucker, B.J.1    Breaker, R.R.2
  • 10
    • 60349104299 scopus 로고    scopus 로고
    • The spliceosome: Design principles of a dynamic RNP machine
    • Wahl, M. C.; Will, C. L.; Lührmann, R. The spliceosome: Design principles of a dynamic RNP machine Cell 2009, 136, 701-718
    • (2009) Cell , vol.136 , pp. 701-718
    • Wahl, M.C.1    Will, C.L.2    Lührmann, R.3
  • 11
    • 0019964240 scopus 로고
    • Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum
    • Walter, P.; Blobel, G. Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum Nature 1982, 299, 691-698
    • (1982) Nature , vol.299 , pp. 691-698
    • Walter, P.1    Blobel, G.2
  • 12
    • 33745586429 scopus 로고    scopus 로고
    • Versatile roles of small RNA regulators in bacteria
    • 3rd ed. Gesteland, R. F. Cech, T. R. Atkins, J. F. Cold Spring Harbor Laboratory Press: Cold Spring Harbor
    • Gottesman, G. S. a. S. Versatile roles of small RNA regulators in bacteria. In The RNA World, 3rd ed.; Gesteland, R. F.; Cech, T. R.; Atkins, J. F., Eds., Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 2006; pp 567-594.
    • (2006) The RNA World , pp. 567-594
    • Gottesman, G.S.A.S.1
  • 13
    • 2942715028 scopus 로고    scopus 로고
    • Analysis of global conformational transitions in ribozymes
    • Lilley, D. M. J. Analysis of global conformational transitions in ribozymes Methods Mol. Biol. 2004, 252, 77-108
    • (2004) Methods Mol. Biol. , vol.252 , pp. 77-108
    • Lilley, D.M.J.1
  • 14
    • 0042424707 scopus 로고    scopus 로고
    • Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
    • Tama, F.; Valle, M.; Frank, J.; Brooks, C. L. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy Proc. Natl. Acad. Sci. U.S.A 2003, 100, 9319-9323
    • (2003) Proc. Natl. Acad. Sci. U.S.A , vol.100 , pp. 9319-9323
    • Tama, F.1    Valle, M.2    Frank, J.3    Brooks, C.L.4
  • 15
    • 0032931788 scopus 로고    scopus 로고
    • Dynamics of translation on the ribosome: Molecular mechanics of translocation
    • Rodnina, M. V.; Savelsbergh, A.; Wintermeyer, W. Dynamics of translation on the ribosome: Molecular mechanics of translocation FEMS Microbiol. Rev. 1999, 23, 317-333
    • (1999) FEMS Microbiol. Rev. , vol.23 , pp. 317-333
    • Rodnina, M.V.1    Savelsbergh, A.2    Wintermeyer, W.3
  • 16
    • 6344252614 scopus 로고    scopus 로고
    • Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation
    • Peske, F.; Savelsbergh, A.; Katunin, V. I.; Rodnina, M. V.; Wintermeyer, W. Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation J. Mol. Biol. 2004, 343, 1183-1194
    • (2004) J. Mol. Biol. , vol.343 , pp. 1183-1194
    • Peske, F.1    Savelsbergh, A.2    Katunin, V.I.3    Rodnina, M.V.4    Wintermeyer, W.5
  • 17
    • 0035670662 scopus 로고    scopus 로고
    • Elongation factor G-induced structural change in helix 34 of 16S rRNA related to translocation on the ribosome
    • Matassova, A. B.; Rodnina, M. V.; Wintermeyer, W. Elongation factor G-induced structural change in helix 34 of 16S rRNA related to translocation on the ribosome RNA 2001, 7, 1879-1885
    • (2001) RNA , vol.7 , pp. 1879-1885
    • Matassova, A.B.1    Rodnina, M.V.2    Wintermeyer, W.3
  • 18
    • 0029825658 scopus 로고    scopus 로고
    • Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic
    • Fourmy, D.; Recht, M. I.; Blanchard, S. C.; Puglisi, J. D. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic Science 1996, 274, 1367-1371
    • (1996) Science , vol.274 , pp. 1367-1371
    • Fourmy, D.1    Recht, M.I.2    Blanchard, S.C.3    Puglisi, J.D.4
  • 19
    • 84875969059 scopus 로고    scopus 로고
    • Connecting the kinetics and energy landscape of tRNA translocation on the ribosome
    • 10.1371/journal.pcbi.1003003
    • Whitford, P. C.; Blanchard, S. C.; Cate, J. H. D.; Sanbonmatsu, K. Y. Connecting the kinetics and energy landscape of tRNA translocation on the ribosome PLoS Comput. Biol. 2013, 9 10.1371/journal.pcbi.1003003
    • (2013) PLoS Comput. Biol. , vol.9
    • Whitford, P.C.1    Blanchard, S.C.2    Cate, J.H.D.3    Sanbonmatsu, K.Y.4
  • 20
    • 84861765128 scopus 로고    scopus 로고
    • Computational studies of molecular machines: The ribosome
    • Sanbonmatsu, K. Y. Computational studies of molecular machines: The ribosome Curr. Opin. Struct. Biol. 2012, 22, 168-174
    • (2012) Curr. Opin. Struct. Biol. , vol.22 , pp. 168-174
    • Sanbonmatsu, K.Y.1
  • 21
    • 33846972283 scopus 로고    scopus 로고
    • NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: Probing the structural features that shape the thermodynamic stability of GA pairs
    • Tolbert, B. S.; Kennedy, S. D.; Schroeder, S. J.; Krugh, T. R.; Turner, D. H. NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: Probing the structural features that shape the thermodynamic stability of GA pairs Biochemistry 2007, 46, 1511-1522
    • (2007) Biochemistry , vol.46 , pp. 1511-1522
    • Tolbert, B.S.1    Kennedy, S.D.2    Schroeder, S.J.3    Krugh, T.R.4    Turner, D.H.5
  • 22
    • 0029744135 scopus 로고    scopus 로고
    • Solution structure of (rGCGGACGC)2 by two-dimensional NMR and the iterative relaxation matrix approach
    • Wu, M.; Turner, D. H. Solution structure of (rGCGGACGC)2 by two-dimensional NMR and the iterative relaxation matrix approach Biochemistry 1996, 35, 9677-9689
    • (1996) Biochemistry , vol.35 , pp. 9677-9689
    • Wu, M.1    Turner, D.H.2
  • 29
    • 0032922174 scopus 로고    scopus 로고
    • A modified version of the Cornell et al. Force field with improved sugar pucker phases and helical repeat
    • Cheatham, T. E.; Cieplak, P.; Kollman, P. A. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat J. Biomol. Struct. Dyn. 1999, 16, 845-862
    • (1999) J. Biomol. Struct. Dyn. , vol.16 , pp. 845-862
    • Cheatham, T.E.1    Cieplak, P.2    Kollman, P.A.3
  • 30
    • 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, P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21, 1049-1074
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 31
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers
    • Pérez, A.; Marchán, I.; Svozil, D.; Sponer, J.; Cheatham Iii, T. E.; Laughton, C. A.; Orozco, M. Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers Biophys. J. 2007, 92, 3817-3829
    • (2007) Biophys. J. , vol.92 , pp. 3817-3829
    • Pérez, A.1    Marchán, I.2    Svozil, D.3    Sponer, J.4    Cheatham III, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 32
    • 77952368283 scopus 로고    scopus 로고
    • Reparameterization of RNA χ torsion parameters for the AMBER force field and comparison to NMR spectra for cytidine and uridine
    • Yildirim, I.; Stern, H. A.; Kennedy, S. D.; Tubbs, J. D.; Turner, D. H. Reparameterization of RNA χ torsion parameters for the AMBER force field and comparison to NMR spectra for cytidine and uridine J. Chem. Theory Comput. 2010, 6, 1520-1531
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1520-1531
    • Yildirim, I.1    Stern, H.A.2    Kennedy, S.D.3    Tubbs, J.D.4    Turner, D.H.5
  • 33
    • 80052820313 scopus 로고    scopus 로고
    • Refinement of the Cornell et al. Nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles
    • Zgarbová, M.; Otyepka, M.; Sponer, J.; Mládek, A.; Banáš, P.; Cheatham, T. E., 3rd; Jurečka, P. Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles J. Chem. Theory Comput. 2011, 7, 2886-2902
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2886-2902
    • Zgarbová, M.1    Otyepka, M.2    Sponer, J.3    Mládek, A.4    Banáš, P.5    Cheatham III, T.E.6    Jurečka, P.7
  • 34
    • 84885818229 scopus 로고    scopus 로고
    • High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations
    • 10.1073/pnas.1309392110
    • Chen, A. A.; García, A. E. High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations Proc. Natl. Acad. Sci. U.S.A. 2013, 10.1073/pnas.1309392110
    • (2013) Proc. Natl. Acad. Sci. U.S.A.
    • Chen, A.A.1    García, A.E.2
  • 35
    • 84855661433 scopus 로고    scopus 로고
    • Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium
    • Hart, K.; Foloppe, N.; Baker, C. M.; Denning, E. J.; Nilsson, L.; MacKerell, A. D. Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium J. Chem. Theory Comput. 2012, 8, 348-362
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 348-362
    • Hart, K.1    Foloppe, N.2    Baker, C.M.3    Denning, E.J.4    Nilsson, L.5    MacKerell, A.D.6
  • 36
    • 0348244547 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
    • Foloppe, N.; MacKerell, J. A. D. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data J. Comput. Chem. 2000, 21, 86-104
    • (2000) J. Comput. Chem. , vol.21 , pp. 86-104
    • Foloppe, N.1    MacKerell, J.A.D.2
  • 37
    • 79955484353 scopus 로고    scopus 로고
    • Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
    • Denning, E. J.; Priyakumar, U. D.; Nilsson, L.; Mackerell, A. D. Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA J. Comput. Chem. 2011, 32, 1929-1943
    • (2011) J. Comput. Chem. , vol.32 , pp. 1929-1943
    • Denning, E.J.1    Priyakumar, U.D.2    Nilsson, L.3    MacKerell, A.D.4
  • 38
    • 73549094953 scopus 로고    scopus 로고
    • Effects of restrained sampling space and nonplanar amino groups on free-energy predictions for RNA with imino and sheared tandem GA base pairs flanked by GC, CG, iGiC, or iCiG base pairs
    • Yildirim, I.; Stern, H. A.; Sponer, J.; Spackova, N.; Turner, D. H. Effects of restrained sampling space and nonplanar amino groups on free-energy predictions for RNA with imino and sheared tandem GA base pairs flanked by GC, CG, iGiC, or iCiG base pairs J. Chem. Theory Comput. 2009, 5, 2088-2100
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 2088-2100
    • Yildirim, I.1    Stern, H.A.2    Sponer, J.3    Spackova, N.4    Turner, D.H.5
  • 39
    • 0002594455 scopus 로고    scopus 로고
    • Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases
    • Šponer, J.; Leszczynski, J.; Hobza, P. Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases Biopolymers 2001, 61, 3-31
    • (2001) Biopolymers , vol.61 , pp. 3-31
    • Šponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 40
    • 84873892798 scopus 로고    scopus 로고
    • Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: Molecular dynamics thermodynamics integration study
    • Krepl, M.; Otyepka, M.; Banáš, P.; Šponer, J. Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: Molecular dynamics thermodynamics integration study J. Phys. Chem. B 2013, 117, 1872-1879
    • (2013) J. Phys. Chem. B , vol.117 , pp. 1872-1879
    • Krepl, M.1    Otyepka, M.2    Banáš, P.3    Šponer, J.4
  • 42
    • 0000965687 scopus 로고    scopus 로고
    • Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations
    • Hobza, P.; Šponer, J. Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations Chem. Rev. 1999, 99, 3247-3276
    • (1999) Chem. Rev. , vol.99 , pp. 3247-3276
    • Hobza, P.1    Šponer, J.2
  • 43
    • 80052820313 scopus 로고    scopus 로고
    • Refinement of the Cornell et al. Nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles
    • Zgarbova, M.; Otyepka, M.; Šponer, J.; Mladek, A.; Banáš, P.; Cheatham, T. E.; Jurecka, P. Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles J. Chem. Theory Comput. 2011, 7, 2886-2902
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2886-2902
    • Zgarbova, M.1    Otyepka, M.2    Šponer, J.3    Mladek, A.4    Banáš, P.5    Cheatham, T.E.6    Jurecka, P.7
  • 44
    • 0027146665 scopus 로고
    • Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics
    • Santa Lucia, J.; Turner, D. H. Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics Biochemistry 1993, 32, 12612-12623
    • (1993) Biochemistry , vol.32 , pp. 12612-12623
    • Santa Lucia, J.1    Turner, D.H.2
  • 45
    • 34547357210 scopus 로고    scopus 로고
    • Stacking effects on local structure in RNA: Changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC Pairs
    • Chen, G.; Kierzek, R.; Yildirim, I.; Krugh, T. R.; Turner, D. H.; Kennedy, S. D. Stacking effects on local structure in RNA: Changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC Pairs J. Phys. Chem. B 2007, 111, 6718-6727
    • (2007) J. Phys. Chem. B , vol.111 , pp. 6718-6727
    • Chen, G.1    Kierzek, R.2    Yildirim, I.3    Krugh, T.R.4    Turner, D.H.5    Kennedy, S.D.6
  • 46
    • 80755150263 scopus 로고    scopus 로고
    • Molecular mechanics investigation of an adenine-adenine non-canonical pair conformational change
    • Van Nostrand, K. P.; Kennedy, S. D.; Turner, D. H.; Mathews, D. H. Molecular mechanics investigation of an adenine-adenine non-canonical pair conformational change J. Chem. Theory Comput. 2011, 7, 3779-3792
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 3779-3792
    • Van Nostrand, K.P.1    Kennedy, S.D.2    Turner, D.H.3    Mathews, D.H.4
  • 49
    • 0034506266 scopus 로고    scopus 로고
    • Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions
    • Toukmaji, A.; Sagui, C.; Board, J.; Darden, T. Efficient particle-mesh Ewald based approach to fixed and induced dipolar interactions J. Chem. Phys. 2000, 113, 10913-10927
    • (2000) J. Chem. Phys. , vol.113 , pp. 10913-10927
    • Toukmaji, A.1    Sagui, C.2    Board, J.3    Darden, T.4
  • 50
    • 0942288583 scopus 로고    scopus 로고
    • Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations
    • Sagui, C.; Pedersen, L. G.; Darden, T. A. Towards an accurate representation of electrostatics in classical force fields: Efficient implementation of multipolar interactions in biomolecular simulations J. Chem. Phys. 2004, 120, 73-87
    • (2004) J. Chem. Phys. , vol.120 , pp. 73-87
    • Sagui, C.1    Pedersen, L.G.2    Darden, T.A.3
  • 51
    • 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
  • 52
    • 84986440341 scopus 로고
    • Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
    • Miyamoto, S.; Kollman, P. A. Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models J. Comput. Chem. 1992, 13, 952-962
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 53
    • 33645100816 scopus 로고    scopus 로고
    • Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair
    • Mathews, D. H.; Case, D. A. Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair J. Mol. Biol. 2006, 357, 1683-1693
    • (2006) J. Mol. Biol. , vol.357 , pp. 1683-1693
    • Mathews, D.H.1    Case, D.A.2
  • 54
    • 73049090285 scopus 로고    scopus 로고
    • A partial nudged elastic band implementation for use with large or explicitly solvated systems
    • Bergonzo, C.; Campbell, A. J.; Walker, R. C.; Simmerling, C., A partial nudged elastic band implementation for use with large or explicitly solvated systems. Int. J. Quantum Chem. 2009, 109.
    • (2009) Int. J. Quantum Chem. , vol.109
    • Bergonzo, C.1    Campbell, A.J.2    Walker, R.C.3    Simmerling, C.4
  • 55
    • 14244273182 scopus 로고    scopus 로고
    • Theory and applications of the generalized born solvation model in macromolecular simulations
    • Tsui, V.; Case, D. A. Theory and applications of the generalized born solvation model in macromolecular simulations Biopolymers 2000, 56, 275-291
    • (2000) Biopolymers , vol.56 , pp. 275-291
    • Tsui, V.1    Case, D.A.2
  • 57
    • 84986497803 scopus 로고
    • Multidimensional free-energy calculations using the weighted histogram analysis method
    • Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. Multidimensional free-energy calculations using the weighted histogram analysis method J. Comput. Chem. 1995, 16, 1339-1350
    • (1995) J. Comput. Chem. , vol.16 , pp. 1339-1350
    • Kumar, S.1    Rosenberg, J.M.2    Bouzida, D.3    Swendsen, R.H.4    Kollman, P.A.5
  • 58
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • Roux, B. The calculation of the potential of mean force using computer simulations Comput. Phys. Commun. 1995, 91, 275-282
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 275-282
    • Roux, B.1
  • 59
    • 84896292585 scopus 로고    scopus 로고
    • WHAM: The Weighted Histogram Analysis Method, version 2.0.7; (accessed May 10.
    • Grossfield, A. WHAM: The Weighted Histogram Analysis Method, version 2.0.7; http://membrane.urmc.rochester.edu/content/wham (accessed May 10, 2013).
    • (2013)
    • Grossfield, A.1
  • 60
    • 79957744584 scopus 로고    scopus 로고
    • Computer review of ChemDraw Ultra 12.0
    • Cousins, K. R. Computer review of ChemDraw Ultra 12.0 J. Am. Chem. Soc. 2011, 133, 8388-8388
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 8388-8388
    • Cousins, K.R.1
  • 63
    • 79960650298 scopus 로고    scopus 로고
    • Benchmarking AMBER force fields for RNA: Comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions
    • Yildirim, I.; Stern, H. A.; Tubbs, J. D.; Kennedy, S. D.; Turner, D. H. Benchmarking AMBER force fields for RNA: Comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions J. Phys. Chem. B 2011, 115, 9261-9270
    • (2011) J. Phys. Chem. B , vol.115 , pp. 9261-9270
    • Yildirim, I.1    Stern, H.A.2    Tubbs, J.D.3    Kennedy, S.D.4    Turner, D.H.5
  • 64
    • 84863694548 scopus 로고    scopus 로고
    • The Amber ff99 force field predicts relative free energy changes for RNA helix formation
    • Spasic, A.; Serafini, J.; Mathews, D. H. The Amber ff99 force field predicts relative free energy changes for RNA helix formation J. Chem. Theory Comput. 2012, 8, 2497-2505
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2497-2505
    • Spasic, A.1    Serafini, J.2    Mathews, D.H.3
  • 65
    • 0037102491 scopus 로고    scopus 로고
    • The non-Watson-Crick base pairs and their associated isostericity matrices
    • Leontis, N. B.; Stombaugh, J.; Westhof, E. The non-Wat son-Crick base pairs and their associated isostericity matrices Nucleic Acids Res. 2002, 30, 3497-3531
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3497
    • Leontis, N.B.1    Stombaugh, J.2    Westhof, E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.