메뉴 건너뛰기




Volumn , Issue , 2006, Pages 45-71

Using AMBER to simulate DNA and RNA

Author keywords

AMBER; biomolecular simulation; DNA; Ewald; force fields; MMPBSA; molecular dynamics; RNA

Indexed keywords


EID: 84889972815     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4020-4851-3_2     Document Type: Chapter
Times cited : (11)

References (115)
  • 1
    • 0001555216 scopus 로고
    • A molecular dynamics simulation of double-helical b-dna including counterions and water
    • Seibel, G.L., U.C. Singh, and P.A. Kollman (1985). A molecular dynamics simulation of double-helical B-DNA including counterions and water. Proc. Nat. Acad. Sci. 82, 6537-6540.
    • (1985) Proc. Nat. Acad. Sci. , vol.82 , pp. 6537-6540
    • Seibel, G.L.1    Singh, U.C.2    Kollman, P.A.3
  • 2
    • 0037453255 scopus 로고    scopus 로고
    • Understanding discrimination by the ribosome: Stability testing and goove measurement of codon-anticodon pairs
    • Sanbonmatsu, K.Y. and S. Joseph (2003). Understanding discrimination by the ribosome: Stability testing and goove measurement of codon-anticodon pairs. J. Mol. Biol. 328, 33-47.
    • (2003) J. Mol. Biol. , vol.328 , pp. 33-47
    • Sanbonmatsu, K.Y.1    Joseph, S.2
  • 3
    • 16644372753 scopus 로고    scopus 로고
    • Atomic model of the thermus thermophilus 70s ribosome developed in silico
    • Tung, C.S. and K.Y. Sanbonmatsu (2004). Atomic model of the Thermus thermophilus 70S ribosome developed in silico. Biophys J. 87, 2714-2722.
    • (2004) Biophys J. , vol.87 , pp. 2714-2722
    • Tung, C.S.1    Sanbonmatsu, K.Y.2
  • 4
    • 0029011701 scopus 로고
    • A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
    • Cornell, W.D., et al. (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Amer. Chem. Soc. 117, 5179-5197.
    • (1995) J. Amer. Chem. Soc. , vol.117 , pp. 5179-5197
    • Cornell, W.D.1
  • 5
    • 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., III, P. Cieplak, and P.A. Kollman (1999). A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J. Biomol. Struct. Dyn. 16, 845-862.
    • (1999) J. Biomol. Struct. Dyn. , vol.16 , pp. 845-862
    • Cheatham Iii., T.E.1    Cieplak, P.2    Kollman, P.A.3
  • 6
    • 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., P. Cieplak, and P.A. Kollman (2000). How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comp. Chem. 21, 1049-1074.
    • (2000) J. Comp. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 7
    • 33846823909 scopus 로고
    • Particle mesh ewald-an n log(n) method for ewald sums in large systems
    • Darden, T.A., D.M. York, and L.G. Pedersen (1993). Particle mesh Ewald-An N log(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.A.1    York, D.M.2    Pedersen, L.G.3
  • 9
    • 0029170114 scopus 로고
    • Molecular dynamics simulations on solvated biomolecular systems-the particle mesh ewald method leads to stable trajectories of dna, rna and proteins
    • Cheatham, T.E., III, J.L. Miller, T. Fox, T.A. Darden, and P.A. Kollman (1995). Molecular dynamics simulations on solvated biomolecular systems-The particle mesh Ewald method leads to stable trajectories of DNA, RNA and proteins. J. Amer. Chem. Soc. 117, 4193-4194.
    • (1995) J. Amer. Chem. Soc. , vol.117 , pp. 4193-4194
    • Cheatham, T.E.1    Miller, L.I.J.2    Fox, T.3    Darden, T.A.4    Kollman, P.A.5
  • 10
    • 0029110156 scopus 로고
    • Toward accurate modeling of dna: The importance of long-range electrostatics
    • York, D.M., W. Yang, H. Lee, T.A. Darden, and L. Pedersen (1995). Toward accurate modeling of DNA: The importance of long-range electrostatics. J. Amer. Chem. Soc. 117, 5001-5002.
    • (1995) J. Amer. Chem. Soc. , vol.117 , pp. 5001-5002
    • York, D.M.1    Yang, W.2    Lee, H.3    Darden, T.A.4    Pedersen, L.5
  • 11
    • 0029941154 scopus 로고    scopus 로고
    • Observation of the a-dna to b-dna transition during unrestrained molecular dynamics in aqueous solution
    • Cheatham, T.E., III and P.A. Kollman (1996). Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J. Mol. Biol. 259, 434-444.
    • (1996) J. Mol. Biol. , vol.259 , pp. 434-444
    • Cheatham Iii., T.E.1    Kollman, P.A.2
  • 12
    • 0030953141 scopus 로고    scopus 로고
    • Molecular dynamics simulations highlight the structural differences in dna:dna, rna:rna and dna:rna hybrid duplexes
    • Cheatham, T.E., III and P.A. Kollman (1997). Molecular dynamics simulations highlight the structural differences in DNA:DNA, RNA:RNA and DNA:RNA hybrid duplexes. J. Amer. Chem. Soc. 119, 4805-4825.
    • (1997) J. Amer. Chem. Soc. , vol.119 , pp. 4805-4825
    • Cheatham Iii., T.E.1    Kollman, P.A.2
  • 13
    • 0031572854 scopus 로고    scopus 로고
    • Insight into the stabilization of a-dna by specific ion association: Spontaneous b-dna to a-dna transitions observed in molecular dynamics simulations of d[acccgcgggt]2 in the presence of hexaammine cobalt(iii
    • Cheatham, T.E., III and P.A. Kollman (1997). Insight into the stabilization of A-DNA by specific ion association: Spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaammine cobalt(III). Structure 5, 1297-1311.
    • (1997) Structure , vol.5 , pp. 1297-1311
    • Cheatham Iii., T.E.1    Kollman, P.A.2
  • 14
    • 0030862276 scopus 로고    scopus 로고
    • A 5-nanosecond molecular dynamics trajectory for b-dna: Analysis of structure, motions and solvation
    • Young, M.A., G. Ravishanker, and D.L. Beveridge (1997). A 5-nanosecond molecular dynamics trajectory for B-DNA: Analysis of structure, motions and solvation. Biophys. J. 73, 2313-2336.
    • (1997) Biophys. J. , vol.73 , pp. 2313-2336
    • Young, M.A.1    Ravishanker, G.2    Beveridge, D.L.3
  • 15
    • 0002042326 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids in solution: How sensitive are the results to small perturbations in the force field and environment
    • M Sarma and R. Sarma, Editors, Adenine Press: Schenectady, NY
    • Cheatham, T.E., III and P.A. Kollman (1998). Molecular dynamics simulation of nucleic acids in solution: How sensitive are the results to small perturbations in the force field and environment, in Structure, motion, interactions and expression of biological macromolecules, M. Sarma and R. Sarma, Editors, Adenine Press: Schenectady, NY. p. 99-116.
    • (1998) Structure, Motion, Interactions and Expression of Biological Macromolecules , pp. 99-116
    • Cheatham Iii., T.E.1    Kollman, P.A.2
  • 16
    • 0000115258 scopus 로고    scopus 로고
    • Molecular dynamics studies of the conformational preferences of a dna double helix in water and an ethanol/water mixture: Theoretical considerations of the a→b transition
    • Sprous, D., M.A. Young, and D.L. Beveridge (1998). Molecular dynamics studies of the conformational preferences of a DNA double helix in water and an ethanol/water mixture: Theoretical considerations of the A→B transition. J. Phys. Chem. B. 102, 4658-4667.
    • (1998) J. Phys. Chem. B. , vol.102 , pp. 4658-4667
    • Sprous, D.1    Young, M.A.2    Beveridge, D.L.3
  • 17
    • 0032575760 scopus 로고    scopus 로고
    • Molecular dynamics simulations of an oligonucleotide duplex with adenine-tracts phased by a full helix turn
    • Young, M.A. and D.L. Beveridge (1998). Molecular dynamics simulations of an oligonucleotide duplex with adenine-tracts phased by a full helix turn. J. Mol. Biol. 281, 675-687.
    • (1998) J. Mol. Biol. , vol.281 , pp. 675-687
    • Young, M.A.1    Beveridge, D.L.2
  • 18
    • 10044257912 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the 136 unique tetranucleotide sequences of dna oligonucleotides. i. research design and results on d(cpg) steps
    • Beveridge, D.L., et al. (2004). Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. Biophys. J. 87, 3799-3813.
    • (2004) Biophys. J. , vol.87 , pp. 3799-3813
    • Beveridge, D.L.1
  • 19
    • 0344778061 scopus 로고
    • Semi analytical treatment of solvation for molecular mechanics and dynamics
    • Still, W.C., A. Tempczyk, R.C. Hawley, and T. Hendrickson (1990). Semi analytical treatment of solvation for molecular mechanics and dynamics. J. Amer. Chem. Soc. 112, 6127-6128.
    • (1990) J. Amer. Chem. Soc. , vol.112 , pp. 6127-6128
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 20
    • 0002636134 scopus 로고
    • Pairwise solute descreening of solute charges from a dielectric medium
    • Hawkins, G.D., C.J. Cramer, and D.G. Truhlar (1995). Pairwise solute descreening of solute charges from a dielectric medium. Chem. Phys. Lett. 246, 122-129.
    • (1995) Chem. Phys. Lett. , vol.246 , pp. 122-129
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 21
    • 14244273182 scopus 로고    scopus 로고
    • Theory and applications of the generalized born solvation model in macromolecular simulations
    • Tsui, V. and D.A. Case (2001). Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopol. 56, 275-291.
    • (2001) Biopol. , vol.56 , pp. 275-291
    • Tsui, V.1    Case, D.A.2
  • 22
    • 0034701222 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acids with a generalized born solvation model
    • Tsui, V. and D.A. Case (2000). Molecular dynamics simulations of nucleic acids with a generalized Born solvation model. J. Amer. Chem. Soc. 122, 2489-2498.
    • (2000) J. Amer. Chem. Soc. , vol.122 , pp. 2489-2498
    • Tsui, V.1    Case, D.A.2
  • 24
    • 0029633186 scopus 로고
    • 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
    • Pearlman, D.A., D.A. Case, J.W. Caldwell, W.S. Ross, T.E. Cheatham, S. Debolt, D. Ferguson, G. Seibel, and P. Kollman (1995). 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. 91, 1-41.
    • (1995) Comp. Phys. Comm. , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.S.4    Cheatham, T.E.5    Debolt, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.9
  • 25
    • 23444454552 scopus 로고    scopus 로고
    • The amber biomolecular simulation programs
    • Case, D.A., et al. (2005). The AMBER biomolecular simulation programs. J. Comp. Chem. 26, 1668-1688.
    • (2005) J. Comp. Chem. , vol.26 , pp. 1668-1688
    • Case, D.A.1
  • 26
    • 0034036078 scopus 로고    scopus 로고
    • Nucleic acids: Theory and computer simulation, y2k
    • Beveridge, D.L. and K.J. McConnell (2000). Nucleic acids: Theory and computer simulation, Y2K. Cur. Op. Struct. Biol. 10, 182-196.
    • (2000) Cur. Op. Struct. Biol. , vol.10 , pp. 182-196
    • Beveridge, D.L.1    McConnell, K.J.2
  • 27
    • 0033654654 scopus 로고    scopus 로고
    • Molecular dynamics simulation of nucleic acids
    • Cheatham, T.E., III and P.A. Kollman (2000). Molecular dynamics simulation of nucleic acids. Ann. Rev. Phys. Chem. 51, 435-471.
    • (2000) Ann. Rev. Phys. Chem. , vol.51 , pp. 435-471
    • Cheatham III, T.E.1    Kollman, P.A.2
  • 28
    • 1242347628 scopus 로고    scopus 로고
    • Theoretical methods for the simulation of nucleic acids
    • Orozco, M., A. Perez, A. Noy, and F. Javier Luque (2003). Theoretical methods for the simulation of nucleic acids. Chem. Soc. Rev. 32, 350-364.
    • (2003) Chem. Soc. Rev. , vol.32 , pp. 350-364
    • Orozco, M.1    Perez, A.2    Noy, A.3    Javier Luque, F.4
  • 29
    • 2942547665 scopus 로고    scopus 로고
    • Simulation and modeling of nucleic acid structure, dynamics and interactions
    • Cheatham, T.E., III (2004). Simulation and modeling of nucleic acid structure, dynamics and interactions. Cur. Opin. Struct. Biol. 14, 360-367.
    • (2004) Cur. Opin. Struct. Biol. , vol.14 , pp. 360-367
    • Cheatham Iii., T.E.1
  • 30
    • 33847651004 scopus 로고    scopus 로고
    • Molecular modeling and atomistic simulation of nucleic acids
    • Cheatham, T.E., III (2005). Molecular modeling and atomistic simulation of nucleic acids. Ann. Reports Comp. Chem. 1, 75-89.
    • (2005) Ann. Reports Comp. Chem. , vol.1 , pp. 75-89
    • Cheatham III, T.E.1
  • 31
    • 0036280718 scopus 로고    scopus 로고
    • Molecular dynamics applied to nucleic acids
    • Norberg, J. and L. Nilsson (2002). Molecular dynamics applied to nucleic acids. Acc. Chem. Res. 35, 465-472.
    • (2002) Acc. Chem. Res. , vol.35 , pp. 465-472
    • Norberg, J.1    Nilsson, L.2
  • 32
    • 14244271476 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acids: Successes, limitations and promise
    • Cheatham, T.E., III and M.A. Young (2001). Molecular dynamics simulations of nucleic acids: Successes, limitations and promise. Biopolymers 56, 232-256.
    • (2001) Biopolymers , vol.56 , pp. 232-256
    • Cheatham Iii., T.E.1    Young, M.A.2
  • 33
    • 4444351490 scopus 로고    scopus 로고
    • Empirical force fields for biological macromolecules: Overview and issues
    • MacKerell, A.D., Jr. (2004). Empirical force fields for biological macromolecules: Overview and issues. J. Comp. Chem. 25, 1584-1604.
    • (2004) J. Comp. Chem. , vol.25 , pp. 1584-1604
    • MacKerell Jr., A.D.1
  • 34
    • 0037342509 scopus 로고    scopus 로고
    • DNA polymorphism: A comparison of force fields for nucleic acids
    • Reddy, S.Y., F. Leclerc, and M. Karplus (2003). DNA polymorphism: A comparison of force fields for nucleic acids. Biophys. J. 84, 1421-1449.
    • (2003) Biophys. J. , vol.84 , pp. 1421-1449
    • Reddy, S.Y.1    Leclerc, F.2    Karplus, M.3
  • 35
    • 0032459726 scopus 로고    scopus 로고
    • Molecular dynamics simulations of environment and sequence dependent dna conformation: The development of the bms nucleic acid force field and comparison with experimental results
    • Langley, D.R. (1998). Molecular dynamics simulations of environment and sequence dependent DNA conformation: The development of the BMS nucleic acid force field and comparison with experimental results. J. Biomol. Struct. Dyn. 16, 487-509.
    • (1998) J. Biomol. Struct. Dyn. , vol.16 , pp. 487-509
    • Langley, D.R.1
  • 37
    • 77956714436 scopus 로고    scopus 로고
    • Molecular modeling of nucleic acid structure
    • S.L. Beaucage, et al., Editors, Wiley: New York
    • Cheatham, T.E., III, B.R. Brooks, and P.A. Kollman (2000). Molecular modeling of nucleic acid structure, in Current Protocols in Nucleic Acid Chemistry, S.L. Beaucage, et al., Editors, Wiley: New York. p. 7.5.1-7.5.12.
    • (2000) Current Protocols in Nucleic Acid Chemistry , pp. 751-7512
    • Cheatham, T.E.1    Brooks, R.I.B.2    Kollman, P.A.3
  • 39
    • 0001041959 scopus 로고    scopus 로고
    • Fast, efficient generation of high quality atomic charges. am1-bcc model: I. method
    • Jakalian, A., B.L. Bush, D.B. Jack, and C.I. Bayly (2000). Fast, efficient generation of high quality atomic charges. AM1-BCC model: I. method. J. Comp. Chem. 21, 132-146.
    • (2000) J. Comp. Chem. , vol.21 , pp. 132-146
    • Jakalian, A.1    Bush, B.L.2    Jack, D.B.3    Bayly, C.I.4
  • 40
    • 0036890178 scopus 로고    scopus 로고
    • Fast, efficient generation of high-quality atomic charges. am1-bcc model: Ii. parameterization and validation
    • Jakalian, A., D.B. Jack, and C.I. Bayly (2002). Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 23, 1623-41.
    • (2002) J Comput Chem , vol.23 , pp. 1623-1641
    • Jakalian, A.1    Jack, D.B.2    Bayly, C.I.3
  • 42
    • 0345983583 scopus 로고    scopus 로고
    • Modeling unusual nucleic acid structures
    • N.B. Leontis and J. Santa Lucia, Editors, ACS: Washington
    • Macke, T. and D.A. Case (1998). Modeling unusual nucleic acid structures, in Molecular modeling of nucleic acids, N.B. Leontis and J. Santa Lucia, Editors, ACS: Washington. p. 379-393.
    • (1998) Molecular Modeling of Nucleic Acids , pp. 379-393
    • MacKe, T.1    Case, D.A.2
  • 43
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • Lu, X.J. and W.K. Olson (2003). 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31, 5108-21.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5108-5121
    • Lu, X.J.1    Olson, W.K.2
  • 44
    • 0030801742 scopus 로고    scopus 로고
    • A new model for the three-dimensional folding of escherichia coli 16 s ribosomal rna. i. fitting the rna to a 3d electron microscopic map at 20 a
    • Mueller, F. and R. Brimacombe (1997). A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 A. J. Mol. Biol. 271, 524-44.
    • (1997) J. Mol. Biol. , vol.271 , pp. 524-544
    • Mueller, F.1    Brimacombe, R.2
  • 46
    • 0032232180 scopus 로고    scopus 로고
    • MANIP: An interactive tool for modelling rna
    • 255-7
    • Massire, C. and E. Westhof (1998). MANIP: An interactive tool for modelling RNA. J. Mol. Graph. Model. 16, 197-205, 255-7.
    • (1998) J. Mol. Graph. Model. , vol.16 , pp. 197-205
    • Massire, C.1    Westhof, E.2
  • 47
    • 0027366671 scopus 로고
    • Reproducing the three-dimensional structure of a trna molecule from structural constraints
    • Major, F., D. Gautheret, and R. Cedergren (1993). Reproducing the three-dimensional structure of a tRNA molecule from structural constraints. Proc. Natl. Acad. Sci. 90, 9408-12.
    • (1993) Proc. Natl. Acad. Sci. , vol.90 , pp. 9408-9412
    • Major, F.1    Gautheret, D.2    Cedergren, R.3
  • 48
    • 0028023784 scopus 로고
    • Nucleic acid modeling tool (namot): An interactive graphic tool for modeling nucleic acid structures
    • Tung, C.S. and E.S. Carter, 2nd (1994). Nucleic acid modeling tool (NAMOT): An interactive graphic tool for modeling nucleic acid structures. Comput. Appl. Biosci. 10, 427-33.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 427-433
    • Tung, C.S.1    Carter II, E.S.2
  • 49
    • 0034808134 scopus 로고    scopus 로고
    • A theoretical study of the aminolysis reaction of lysine 199 of human serum albumin with benzylpenicillin: Consequences for immunochemistry of penicillins
    • Diaz, N., D. Suarez, T.L. Sordo, and K.M. Merz, Jr. (2001). A theoretical study of the aminolysis reaction of lysine 199 of human serum albumin with benzylpenicillin: Consequences for immunochemistry of penicillins. J. Am. Chem. Soc. 123, 7574-83.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 7574-7583
    • Diaz, N.1    Suarez, D.2    Sordo, T.L.3    Merz Jr., K.M.4
  • 50
    • 16244384181 scopus 로고    scopus 로고
    • Hybrid qm/mm and dft investigations of the catalytic mechanism and inhibition of the dinuclear zinc metallo-b-lactamase ccra from bacteroides fragilis
    • Park, H., E.N. Brothers, and K.M. Merz, Jr. (2005). Hybrid QM/MM and DFT investigations of the catalytic mechanism and inhibition of the dinuclear zinc metallo-b-lactamase CcrA from Bacteroides fragilis. J. Am. Chem. Soc. 127, 4232-41.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 4232-4241
    • Park, H.1    Brothers, E.N.2    Merz Jr., K.M.3
  • 51
    • 22944443583 scopus 로고    scopus 로고
    • Isotropic periodic sum: A method for the calculation of long-range interactions
    • Wu, X. and B.R. Brooks (2005). Isotropic periodic sum: A method for the calculation of long-range interactions. J. Chem. Phys. 122, 44107.
    • (2005) J. Chem. Phys. , vol.122 , pp. 44107
    • Wu, X.1    Brooks, B.R.2
  • 52
    • 36449006131 scopus 로고
    • Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations
    • Roitberg, A. and R. Elber (1991). Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations. J. Chem. Phys. 95, 9277-9286.
    • (1991) J. Chem. Phys. , vol.95 , pp. 9277-9286
    • Roitberg, A.1    Elber, R.2
  • 53
    • 0032578192 scopus 로고    scopus 로고
    • Combined locally enhanced sampling and particle mesh ewald as a strategy to locate the experimental structure of a non-helical nucleic acid
    • Simmerling, C., J.L. Miller, and P.A. Kollman (1998). Combined locally enhanced sampling and particle mesh Ewald as a strategy to locate the experimental structure of a non-helical nucleic acid. J. Amer. Chem. Soc. 120, 7149-7155.
    • (1998) J. Amer. Chem. Soc. , vol.120 , pp. 7149-7155
    • Simmerling, C.1    Miller, J.L.2    Kollman, P.A.3
  • 54
    • 1942423619 scopus 로고    scopus 로고
    • MMTSB tool set: Enhanced sampling and multiscale modeling methods for applications in structural biology
    • Feig, M., J. Karanicolas, and C.L. Brooks, 3rd (2004). MMTSB Tool Set: Enhanced sampling and multiscale modeling methods for applications in structural biology. J. Mol. Graph Model 22, 377-95.
    • (2004) J. Mol. Graph Model , vol.22 , pp. 377-395
    • Feig, M.1    Karanicolas, J.2    Brooks Iii., C.L.3
  • 55
    • 0033024177 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules: Long-range electrostatic effects
    • Sagui, C. and T.A. Darden (1999). Molecular dynamics simulations of biomolecules: Long-range electrostatic effects. Ann. Rev. Biophys. Biomol. Struct. 28, 155-179.
    • (1999) Ann. Rev. Biophys. Biomol. Struct. , vol.28 , pp. 155-179
    • Sagui, C.1    Darden, T.A.2
  • 56
    • 84961981091 scopus 로고    scopus 로고
    • Implicit solvation models: Equilibria, structure, spectra, and dynamics
    • Cramer, C.J. and D.G. Truhlar (1999). Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. Chem Rev 99, 2161-2200.
    • (1999) Chem Rev , vol.99 , pp. 2161-2200
    • Cramer, C.J.1    Truhlar, D.G.2
  • 57
    • 0033654297 scopus 로고    scopus 로고
    • Generalized born models of molecular solvation effects
    • Bashford, D. and D.A. Case (2000). Generalized Born models of molecular solvation effects. Ann. Rev. Phys. Chem. 51, 129-152.
    • (2000) Ann. Rev. Phys. Chem. , vol.51 , pp. 129-152
    • Bashford, D.1    Case, D.A.2
  • 58
    • 1942456697 scopus 로고    scopus 로고
    • Recent advances in the development and application of implicit solvent models in biomolecule simulations
    • Feig, M. and C.L.I. Brooks (2004). Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 14, 217-224.
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 217-224
    • Feig, M.1    Brooks, C.L.I.2
  • 59
    • 0037529067 scopus 로고    scopus 로고
    • Electrostatics and dynamics of proteins
    • Simonson, T. (2003). Electrostatics and dynamics of proteins. Rep. Prog. Phys. 66, 737-787.
    • (2003) Rep. Prog. Phys. , vol.66 , pp. 737-787
    • Simonson, T.1
  • 60
    • 1642464809 scopus 로고    scopus 로고
    • Poisson-boltzmann methods for biomolecular electrostatics
    • Baker, N.A. (2004). Poisson-Boltzmann methods for biomolecular electrostatics. Meth. Enzym. 383, 94-118.
    • (2004) Meth. Enzym. , vol.383 , pp. 94-118
    • Baker, N.A.1
  • 61
    • 0842333152 scopus 로고    scopus 로고
    • Implicit solvation based on generalized born theory in different dielectric environments
    • Feig, M., W. Im, and C.L. Brooks, 3rd (2004). Implicit solvation based on generalized Born theory in different dielectric environments. J. Chem. Phys. 120, 903-11.
    • (2004) J. Chem. Phys. , vol.120 , pp. 903-911
    • Feig, M.1    Im, W.2    Brooks III, C.L.3
  • 62
    • 0033468737 scopus 로고    scopus 로고
    • Application of a pairwise generalized born model to proteins and nucleic acids: Inclusion of salt effects
    • Srinivasan, J., M.W. Trevathan, P. Beroza, and D.A. Case (1999). Application of a pairwise generalized Born model to proteins and nucleic acids: Inclusion of salt effects. Theor. Chem. Acc. 101, 426-434.
    • (1999) Theor. Chem. Acc. , vol.101 , pp. 426-434
    • Srinivasan, J.1    Trevathan, M.W.2    Beroza, P.3    Case, D.A.4
  • 63
    • 0000741414 scopus 로고    scopus 로고
    • A modification of the generalized born theory for improved estimates of solvation energies and pk shifts
    • Jayaram, B., Y. Liu, and D.L. Beveridge (1998). A modification of the generalized Born theory for improved estimates of solvation energies and pK shifts. J. Chem. Phys. 109, 1495-1471.
    • (1998) J. Chem. Phys. , vol.109 , pp. 1495-1471
    • Jayaram, B.1    Liu, Y.2    Beveridge, D.L.3
  • 64
    • 0037110472 scopus 로고    scopus 로고
    • Effective born radii in the generalized born approximation: The importance of being perfect
    • Onufriev, A., D.A. Case, and D. Bashford (2002). Effective Born radii in the generalized Born approximation: The importance of being perfect. J. Comp. Chem. 23, 1297-1304.
    • (2002) J. Comp. Chem. , vol.23 , pp. 1297-1304
    • Onufriev, A.1    Case, D.A.2    Bashford, D.3
  • 65
    • 0141453063 scopus 로고    scopus 로고
    • Deficiency of the coulomb-field approximation in the generalized born model: An improved formula for born radii evaluation
    • Grycuk, T. (2003). Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation. J. Comp. Chem. 119, 4817-4826.
    • (2003) J. Comp. Chem. , vol.119 , pp. 4817-4826
    • Grycuk, T.1
  • 66
    • 22944441922 scopus 로고    scopus 로고
    • Incorporating variable dielectric environments into the generalized born model
    • Sigalov, G., P. Scheffel, and A. Onufriev (2005). Incorporating variable dielectric environments into the generalized Born model. J. Chem. Phys. 122, 094511.
    • (2005) J. Chem. Phys. , vol.122 , pp. 094511
    • Sigalov, G.1    Scheffel, P.2    Onufriev, A.3
  • 67
    • 20644449471 scopus 로고    scopus 로고
    • Modification of the generalized born model suitable for macromolecules
    • Onufriev, A., D. Bashford, and D.A. Case (2000). Modification of the generalized Born model suitable for macromolecules. J. Phys. Chem. B. 104, 3712-3720.
    • (2000) J. Phys. Chem. B. , vol.104 , pp. 3712-3720
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 68
    • 20544433165 scopus 로고
    • Van der waals volumes and radii
    • Bondi, A. (1964). van der Waals volumes and radii. J. Phys. Chem. 68, 441-451.
    • (1964) J. Phys. Chem. , vol.68 , pp. 441-451
    • Bondi, A.1
  • 69
    • 0031552979 scopus 로고    scopus 로고
    • Parameterized model for aqueous free energies of solvation using geometry-dependent atomic surface tensions with implicit electrostatics
    • Hawkins, G.D., C.J. Cramer, and D.G. Truhlar (1997). Parameterized model for aqueous free energies of solvation using geometry-dependent atomic surface tensions with implicit electrostatics. J. Phys. Chem. B. 101, 7147-7157.
    • (1997) J. Phys. Chem. B. , vol.101 , pp. 7147-7157
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 70
    • 33748390341 scopus 로고    scopus 로고
    • Parameterized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium
    • Hawkins, G.D., C.J. Cramer, and D.G. Truhlar (1996). Parameterized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium. J. Phys. Chem. 100, 19824-19839.
    • (1996) J. Phys. Chem. , vol.100 , pp. 19824-19839
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 71
    • 0025661993 scopus 로고
    • A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution
    • Schaefer, M. and C. Froemmel (1990). A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution. J Mol Biol 216, 1045-66.
    • (1990) J Mol Biol , vol.216 , pp. 1045-1066
    • Schaefer, M.1    Froemmel, C.2
  • 73
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of dna. rna and phosphoramidate helices
    • Srinivasan, J., T.E. Cheatham, III, P. Cieplak, P.A. Kollman, and D.A. Case (1998). Continuum solvent studies of the stability of DNA, RNA and phosphoramidate helices. J. Amer. Chem. Soc. 120, 9401-9409.
    • (1998) J. Amer. Chem. Soc. , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham, T.E.2    Cieplak, I.P.3    Kollman, P.A.4    Case, D.A.5
  • 74
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • Kollman, P.A., 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
  • 75
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: Es/is, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
    • Vorobjev, Y.N., J.C. Almagro, and J. Hermans (1998). Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins. 32, 399-413.
    • (1998) Proteins. , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 76
    • 0033003955 scopus 로고    scopus 로고
    • ES/is: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model
    • Vorobjev, Y.N. and J. Hermans (1999). ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model. Biophys. Chem. 78, 195-205.
    • (1999) Biophys. Chem. , vol.78 , pp. 195-205
    • Vorobjev, Y.N.1    Hermans, J.2
  • 77
    • 0031008575 scopus 로고    scopus 로고
    • On the calculation of binding free energies using continuum methods: Application to mhc class i protein-peptide interactions
    • Froloff, N., A. Windemuth, and B. Honig (1997). On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions. Prot. Sci. 6, 1293-1301.
    • (1997) Prot. Sci. , vol.6 , pp. 1293-1301
    • Froloff, N.1    Windemuth, A.2    Honig, B.3
  • 78
    • 0031637651 scopus 로고    scopus 로고
    • Ligand binding affinity prediction by linear interaction energy methods
    • Hansson, T., J. Marelius, and J. Aqvist (1998). Ligand binding affinity prediction by linear interaction energy methods. J. Comp. Aided Mol. Des. 12, 27-35.
    • (1998) J. Comp. Aided Mol. Des. , vol.12 , pp. 27-35
    • Hansson, T.1    Marelius, J.2    Aqvist, J.3
  • 79
    • 0028246710 scopus 로고
    • Salt effects on ligand-dna binding. minor groove binding antibiotics
    • Misra, V.K., K.A. Sharp, R.A. Friedman, and B. Honig (1994). Salt effects on ligand-DNA binding. Minor groove binding antibiotics. J. Mol. Biol. 238, 245-263.
    • (1994) J. Mol. Biol. , vol.238 , pp. 245-263
    • Misra, V.K.1    Sharp, K.A.2    Friedman, R.A.3    Honig, B.4
  • 80
    • 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, J. Srinivasan, D.A. Case, and P.A. Kollman (1998). Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J. Biomol. Struct. Dyn. 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
  • 81
    • 0032466648 scopus 로고    scopus 로고
    • Continuum solvent studies of the stanbility of rna hairpin loops and helices
    • Srinivasan, J., J.L. Miller, P.A. Kollman, and D.A. Case (1998). Continuum solvent studies of the stanbility of RNA hairpin loops and helices. J. Biomol. Struct. Dyn. 16, 671-682.
    • (1998) J. Biomol. Struct. Dyn. , vol.16 , pp. 671-682
    • Srinivasan, J.1    Miller, J.L.2    Kollman, P.A.3    Case, D.A.4
  • 82
    • 0037234043 scopus 로고    scopus 로고
    • Free energy calculations for theophylline binding to an rna aptamer: Comparison of mm-pbsa and thermodynamic integration methods
    • Gouda, H., I.D. Kuntz, D.A. Case, and P.A. Kollman (2003). Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. Biopol. 68, 16-34.
    • (2003) Biopol. , vol.68 , pp. 16-34
    • Gouda, H.1    Kuntz, I.D.2    Case, D.A.3    Kollman, P.A.4
  • 83
    • 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, T.E. Cheatham, III, F. Ryjacek, F. Lankaš, L. van Meervelt, P. Hobza, and J. Šponer (2003). 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. Amer. Chem. Soc. 125, 1759-1769.
    • (2003) J. Amer. Chem. Soc. , vol.125 , pp. 1759-1769
    • Spackova, N.1    Cheatham, T.E.2    Ryjacek, I.F.3    Lankaš, F.4    Van Meervelt, L.5    Hobza, P.6    Šponer, J.7
  • 84
    • 0042823487 scopus 로고    scopus 로고
    • Formation pathways of a guanine-quadruplex dna revealed by molecular dynamics and thermodynamical analysis of the substates
    • Stefl, R., T.E. Cheatham, III, N. Spackova, E. Fadrna, I. Berger, J. Koca, and J. Šponer (2003). Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamical analysis of the substates.Biophys. J. 85, 1787-1804.
    • (2003) Biophys. J. , vol.85 , pp. 1787-1804
    • Stefl, R.1    Cheatham, T.E.2    Spackova, I.N.3    Fadrna, E.4    Berger, I.5    Koca, J.6    Šponer, J.7
  • 86
    • 0028850111 scopus 로고
    • Structure determination and analysis of local bending in an a-tract dna duplex: Comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(cgcaaaaatgcg
    • Young, M.A., J. Srinivasan, I. Goljer, S. Kumar, D.L. Beveridge, and P.H. Bolton (1995). Structure determination and analysis of local bending in an A-tract DNA duplex: Comparison of results from crystallography, nuclear magnetic resonance, and molecular dynamics simulation on d(CGCAAAAATGCG). Methods in Enzymology 261, 121-144.
    • (1995) Methods in Enzymology , vol.261 , pp. 121-144
    • Young, M.A.1    Srinivasan, J.2    Goljer, I.3    Kumar, S.4    Beveridge, D.L.5    Bolton, P.H.6
  • 87
    • 0000367525 scopus 로고    scopus 로고
    • Constant pressure molecular dynamics simulations of the dodecamers: D(gcgcgcgcgcgc)2 and r(gcgcgcgcgcgc)2
    • Norberg, J. and L. Nilsson (1996). Constant pressure molecular dynamics simulations of the dodecamers: D(GCGCGCGCGCGC)2 and r(GCGCGCGCGCGC)2. J. Chem. Phys. 104, 6052-6057.
    • (1996) J. Chem. Phys. , vol.104 , pp. 6052-6057
    • Norberg, J.1    Nilsson, L.2
  • 88
    • 0030873459 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the d(tat) triplex helix
    • Shields, G.C., CA. Laughton, and M. Orozco (1997). Molecular dynamics simulations of the d(TAT) triplex helix. J. Amer. Chem. Soc. 119, 7463-7469.
    • (1997) J. Amer. Chem. Soc. , vol.119 , pp. 7463-7469
    • Shields, G.C.1    Laughton, C.A.2    Orozco, M.3
  • 89
  • 90
    • 0031047279 scopus 로고    scopus 로고
    • Intrusion of counterions into the spine of hydration in the minor groove of b-dna: Fractional occupancy of electronegative pockets
    • Young, M.A., B. Jayaram, and D.L. Beveridge (1997). Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets. J. Amer. Chem. Soc. 119, 59-69.
    • (1997) J. Amer. Chem. Soc. , vol.119 , pp. 59-69
    • Young, M.A.1    Jayaram, B.2    Beveridge, D.L.3
  • 91
    • 0030745348 scopus 로고    scopus 로고
    • Unrestrained molecular dynamics of photodamage dna in aqueous solution
    • Spector, T.I., T.E. Cheatham, III, and PA. Kollman (1997). Unrestrained molecular dynamics of photodamage DNA in aqueous solution. J. Amer. Chem. Soc. 119, 7095-7104.
    • (1997) J. Amer. Chem. Soc. , vol.119 , pp. 7095-7104
    • Spector, T.I.1    Cheatham Iii, T.E.2    Kollman, P.A.3
  • 92
    • 0032542519 scopus 로고    scopus 로고
    • Nanosecond molecular dynamics of hybrid triplex and duplex of polycation deoxyribonucleic guanidine strands with a complementary dna strand
    • Luo, J. and T.C. Bruice (1998). Nanosecond molecular dynamics of hybrid triplex and duplex of polycation deoxyribonucleic guanidine strands with a complementary DNA strand. J. Amer. Chem. Soc. 120, 1115-1123.
    • (1998) J. Amer. Chem. Soc. , vol.120 , pp. 1115-1123
    • Luo, J.1    Bruice, T.C.2
  • 93
    • 0031749571 scopus 로고    scopus 로고
    • Molecular dynamics simulation of a pna-dna-pna triple helix in aqueous solution
    • Shields, G.C., CA. Laughton, and M. Orozco (1998). Molecular dynamics simulation of a PNA-DNA-PNA triple helix in aqueous solution. J. Amer. Chem. Soc. 120, 5895-5904.
    • (1998) J. Amer. Chem. Soc. , vol.120 , pp. 5895-5904
    • Shields, G.C.1    Laughton, C.A.2    Orozco, M.3
  • 94
    • 33748674257 scopus 로고    scopus 로고
    • B to a transition of dna on the nanosecond time scale
    • Yang, L.Q. and B.M. Pettitt (1996). B to A transition of DNA on the nanosecond time scale. J. Phys. Chem. 100, 2564-2566.
    • (1996) J. Phys. Chem. , vol.100 , pp. 2564-2566
    • Yang, L.Q.1    Pettitt, B.M.2
  • 95
    • 0030954859 scopus 로고    scopus 로고
    • A molecular level picture of the stabilization of a-dna in mixed ethanol-water solutions
    • Cheatham, T.E., III, M.F. Crowley, T. Fox, and PA. Kollman (1997). A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions. Proc. Natl. Acad. Sci. 94, 9626-9630.
    • (1997) Proc. Natl. Acad. Sci. , vol.94 , pp. 9626-9630
    • Cheatham Iii., T.E.1    Crowley, M.F.2    Fox, T.3    Kollman, P.A.4
  • 96
    • 28044465975 scopus 로고    scopus 로고
    • The dynamics of the b - A transition of natural dna double helices
    • Jose, D. and D. Porschke (2005). The Dynamics of the B-A transition of natural DNA double helices.J. Am. Chem. Soc. 127, 16120-16128.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 16120-16128
    • Jose, D.1    Porschke, D.2
  • 97
    • 2342637689 scopus 로고    scopus 로고
    • Dynamics of the b - A transition of dna double helices
    • Jose, D. and D. Porschke (2004). Dynamics of the B-A transition of DNA double helices. Nuc. Acids Res. 32, 2251-8.
    • (2004) Nuc. Acids Res. , vol.32 , pp. 2251-2258
    • Jose, D.1    Porschke, D.2
  • 98
    • 0242290881 scopus 로고    scopus 로고
    • NA base-pair step deformability inferred from molecular dynamics simulation
    • Lankaš, F., J. Šponer, J. Langowski, and T.E. Cheatham, III (2003). DNA base-pair step deformability inferred from molecular dynamics simulation. Biophys. J. 85, 2872-2883.
    • (2003) Biophys. J. , vol.85 , pp. 2872-2883
    • Lankaš, F.1    Šponer, J.2    Langowski, J.3    Cheatham Iii, T.E.4
  • 99
    • 17844383238 scopus 로고    scopus 로고
    • The b-to a-dna transition and the reorganization of solvent at the dna surface
    • Pastor, N. (2005). The B-to A-DNA transition and the reorganization of solvent at the DNA surface. Biophys. J. 88, 3262-75.
    • (2005) Biophys. J. , vol.88 , pp. 3262-3275
    • Pastor, N.1
  • 100
    • 18644368600 scopus 로고    scopus 로고
    • Free energy landscape of a-dna to b-dna conversion in aqueous solution
    • Banavali, N.K. and B. Roux (2005). Free energy landscape of A-DNA to B-DNA conversion in aqueous solution. J. Am. Chem. Soc. 127, 6866-76.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 6866-6876
    • Banavali, N.K.1    Roux, B.2
  • 101
    • 0037065332 scopus 로고    scopus 로고
    • DNA dynamics in a water drop without counterions
    • Mazur, A.K. (2002). DNA dynamics in a water drop without counterions. J. Am. Chem. Soc 124, 14707-15.
    • (2002) J. Am. Chem. Soc , vol.124 , pp. 14707-14715
    • Mazur, A.K.1
  • 102
    • 0038540969 scopus 로고    scopus 로고
    • Titration in silico of reversible b→a transitions in dna
    • Mazur, A.K. (2003). Titration in silico of reversible B→A transitions in DNA. J. Amer. Chem. Soc. 125, 7849-7859.
    • (2003) J. Amer. Chem. Soc. , vol.125 , pp. 7849-7859
    • Mazur, A.K.1
  • 103
    • 3042734385 scopus 로고    scopus 로고
    • Olecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations
    • Fadrna, E., N. Spackova, R. Stefl, J. Koca, T.E. Cheatham, III, and J. Šponer (2004). Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations. Biophys. J. 87, 227-242.
    • (2004) Biophys. J. , vol.87 , pp. 227-242
    • Fadrna, E.1    Spackova, N.2    Stefl, R.3    Koca, J.4    Cheatham III, T.E.5    Scaron, J.6
  • 106
    • 0038739103 scopus 로고    scopus 로고
    • Dynamically amorphous character of electronic states in poly(da)-poly(dt) dna
    • Lewis, J.P., T.E. Cheatham, III, H. Wang, E.B. Starikov, and O.F. Sankey (2003). Dynamically amorphous character of electronic states in poly(dA)-poly(dT) DNA. J. Phys. Chem. B 107, 2581-2587.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 2581-2587
    • Lewis, J.P.1    Cheatham, T.E.2    Wang, I.H.3    Starikov, E.B.4    Sankey, O.F.5
  • 107
    • 28444490422 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the 136 unique tetranucleotide sequences of dna oligonucleotides. ii. sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
    • [in press]
    • Dixit, S.B., et al. (2005). Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II. Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. Biophys J, [in press].
    • (2005) Biophys J
    • Dixit, S.B.1
  • 108
    • 1842479952 scopus 로고    scopus 로고
    • Exploring protein native states and large-scale conformational changes with a modified generalized born model
    • Onufriev, A., D. Bashford, and D.A. Case (2004). Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55, 383-94.
    • (2004) Proteins , vol.55 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 109
    • 0026869597 scopus 로고
    • Langevin dynamics of peptides: The frictional dependence of isomerization rates of n-acetylalanyl-n'-methylamide
    • Loncharich, R.J., B.R. Brooks, and R.W. Pastor (1992). Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide. Biopolymers 32, 523-35.
    • (1992) Biopolymers , vol.32 , pp. 523-535
    • Loncharich, R.J.1    Brooks, B.R.2    Pastor, R.W.3
  • 110
    • 4043097703 scopus 로고    scopus 로고
    • Experiment vs force fields: Dna conformation from molecular dynamics simulations
    • Feig, M. and B.M. Pettitt (1997). Experiment vs force fields: DNA conformation from molecular dynamics simulations. J. Phys. Chem. 101, 7361-7363.
    • (1997) J. Phys. Chem. , vol.101 , pp. 7361-7363
    • Feig, M.1    Pettitt, B.M.2
  • 111
    • 0008115219 scopus 로고    scopus 로고
    • B→a→b transitions in a molecular dynamics trajectory of low salt dna solution
    • Real, A.N. and R.J. Greenall (2000). B→A→B transitions in a molecular dynamics trajectory of low salt DNA solution. J. Mol. Model. 6, 654-658.
    • (2000) J. Mol. Model. , vol.6 , pp. 654-658
    • Real, A.N.1    Greenall, R.J.2
  • 112
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. theory and range of validity
    • Lipari, G. and A. Szabo (1982). Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104, 4546-4559.
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4546-4559
    • Lipari, G.1    Szabo, A.2
  • 113
    • 0036283096 scopus 로고    scopus 로고
    • Molecular dynamics and nmr spin relaxation in proteins
    • Case, D.A. (2002). Molecular dynamics and NMR spin relaxation in proteins. Acc. Chem. Res. 35, 325-31.
    • (2002) Acc. Chem. Res. , vol.35 , pp. 325-331
    • Case, D.A.1
  • 114
    • 0036234027 scopus 로고    scopus 로고
    • Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized born model, and with explicit water
    • Xia, B., V. Tsui, D.A. Case, H.J. Dyson, and P.E. Wright (2002). Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water. J. Biomol. NMR 22, 317-31.
    • (2002) J. Biomol. NMR , vol.22 , pp. 317-331
    • Xia, B.1    Tsui, V.2    Case, D.A.3    Dyson, H.J.4    Wright, P.E.5
  • 115
    • 0347062349 scopus 로고    scopus 로고
    • Eintroducing electrostatics into protein x-ray structure refinement: Bulk solvent treated as a dielectric continuum
    • Moulinier, L., D.A. Case, and T. Simonson (2003). Reintroducing electrostatics into protein X-ray structure refinement: Bulk solvent treated as a dielectric continuum. Acta Crystallogr D. Biol Crystallogr 59, 2094-103.
    • (2003) Acta Crystallogr D. Biol Crystallogr , vol.59 , pp. 2094-2103
    • Moulinier, L.1    Case, D.A.2    Simonson, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.