메뉴 건너뛰기




Volumn 157, Issue 3, 2007, Pages 470-480

High performance computing in biology: Multimillion atom simulations of nanoscale systems

Author keywords

High performance computing; Molecular dynamics simulation; Ribosome; RNA; RNA structure; Supercomputing

Indexed keywords

RNA;

EID: 33847175935     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2006.10.023     Document Type: Review
Times cited : (150)

References (59)
  • 1
    • 0032907143 scopus 로고    scopus 로고
    • Molecular dynamics simulations of solvated yeast tRNA(Asp)
    • Auffinger P., LouiseMay S., and Westhof E. Molecular dynamics simulations of solvated yeast tRNA(Asp). Biophysical Journal 76 1/pt.1 (1999) 50-64
    • (1999) Biophysical Journal , vol.76 , Issue.1 -PART1 , pp. 50-64
    • Auffinger, P.1    LouiseMay, S.2    Westhof, E.3
  • 2
    • 0032054952 scopus 로고    scopus 로고
    • Simulations of the molecular dynamics of nucleic acids
    • Auffinger P., and Westhof E. Simulations of the molecular dynamics of nucleic acids. Current Opinion in Structural Biology 8 2 (1998) 227-236
    • (1998) Current Opinion in Structural Biology , vol.8 , Issue.2 , pp. 227-236
    • Auffinger, P.1    Westhof, E.2
  • 3
    • 0035793219 scopus 로고    scopus 로고
    • Water and ion binding around r(UpA)(12) and d(TpA)(12) oligomers: Comparison with RNA and DNA (CpG)(12) duplexes
    • Auffinger P., and Westhof E. Water and ion binding around r(UpA)(12) and d(TpA)(12) oligomers: Comparison with RNA and DNA (CpG)(12) duplexes. Journal of Molecular Biology 305 5 (2001) 1057-1072
    • (2001) Journal of Molecular Biology , vol.305 , Issue.5 , pp. 1057-1072
    • Auffinger, P.1    Westhof, E.2
  • 4
    • 0037187806 scopus 로고    scopus 로고
    • Melting of the solvent structure around a RNA duplex: a molecular dynamics simulation study
    • Auffinger P., and Westhof E. Melting of the solvent structure around a RNA duplex: a molecular dynamics simulation study. Biophys. Chem. 95 3 (2002) 203-210
    • (2002) Biophys. Chem. , vol.95 , Issue.3 , pp. 203-210
    • Auffinger, P.1    Westhof, E.2
  • 5
  • 6
    • 0036175994 scopus 로고    scopus 로고
    • Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase
    • Bockmann R.A., and Grubmuller H. Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase. Nature Structural Biology 9 3 (2002) 198-202
    • (2002) Nature Structural Biology , vol.9 , Issue.3 , pp. 198-202
    • Bockmann, R.A.1    Grubmuller, H.2
  • 7
    • 0034704217 scopus 로고    scopus 로고
    • The structural basis for the action of the antibiotics tetracycline; pactamycin; and hygromycin B on the 30S ribosomal subunit
    • Brodersen D.E., Clemons W.M., Carter A.P., Morgan-Warren R.J., Wimberly B.T., and Ramakrishnan V. The structural basis for the action of the antibiotics tetracycline; pactamycin; and hygromycin B on the 30S ribosomal subunit. Cell 103 7 (2000) 1143-1154
    • (2000) Cell , vol.103 , Issue.7 , pp. 1143-1154
    • Brodersen, D.E.1    Clemons, W.M.2    Carter, A.P.3    Morgan-Warren, R.J.4    Wimberly, B.T.5    Ramakrishnan, V.6
  • 8
    • 33847189477 scopus 로고    scopus 로고
    • Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham III, T.E., Wang, J., Ross, W.S., Simmerling, C.L., Darden, T.A., Merz, K.M., Stanton, R.V., Cheng, A.L., Vincent, J.J., Crowley, M., Tsui, V., Gohlke, H., Radmer, R.J., Duan, Y., Pitera, J., Massova, I., Seibel, G.L., Singh, U.C., Weiner, P.K., Kollman, P.A., 2002. AMBER. In University of California, San Francisco, San Francisco.
  • 9
    • 2942547665 scopus 로고    scopus 로고
    • Simulation and modeling of nucleic acid structure, dynamics and interactions
    • Cheatham III T.E. Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol. 14 3 (2004) 360-367
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , Issue.3 , pp. 360-367
    • Cheatham III, T.E.1
  • 11
    • 0028583190 scopus 로고    scopus 로고
    • Clark, T.W., Hanxleden, R.V., McCammon, J.A., Scott, L.R., 1994. Parallelizing molecular dynamics using spatial decomposition Proceedings of the Scalable High-Performance Computing Conference, pp. 95-102.
  • 12
    • 33846823909 scopus 로고
    • Particle Mesh Ewald: An N.Log(N) Method for Ewald Sums in Large Systems
    • Darden T., York D., and Pedersen L. Particle Mesh Ewald: An N.Log(N) Method for Ewald Sums in Large Systems. Journal of Chemical Physics 98 12 (1993) 10089-10092
    • (1993) Journal of Chemical Physics , vol.98 , Issue.12 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 13
    • 0033117830 scopus 로고    scopus 로고
    • Protein dynamics simulations from nanoseconds to microseconds
    • Doniach S., and Eastman P. Protein dynamics simulations from nanoseconds to microseconds. Current Opinion in Structural Biology 9 (1999) 157-163
    • (1999) Current Opinion in Structural Biology , vol.9 , pp. 157-163
    • Doniach, S.1    Eastman, P.2
  • 14
    • 0032561237 scopus 로고    scopus 로고
    • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
    • Duan Y., and Kollman P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282 5389 (1998) 740-744
    • (1998) Science , vol.282 , Issue.5389 , pp. 740-744
    • Duan, Y.1    Kollman, P.A.2
  • 15
    • 5244378389 scopus 로고    scopus 로고
    • FAMUSAMM: An Algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations
    • Eichinger M., Grubmuller H., Heller H., and Tavan P. FAMUSAMM: An Algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations. Journal of Computational Chemistry 18 14 (1997) 1729-1749
    • (1997) Journal of Computational Chemistry , vol.18 , Issue.14 , pp. 1729-1749
    • Eichinger, M.1    Grubmuller, H.2    Heller, H.3    Tavan, P.4
  • 17
    • 33644848399 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the complete satellite tobacco mosaic virus
    • Freddolino P.L., Arkhipov A.S., Larson S.B., McPherson A., and Schulten K. Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure 14 3 (2006) 437-449
    • (2006) Structure , vol.14 , Issue.3 , pp. 437-449
    • Freddolino, P.L.1    Arkhipov, A.S.2    Larson, S.B.3    McPherson, A.4    Schulten, K.5
  • 18
    • 0036428792 scopus 로고    scopus 로고
    • Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics
    • Gao M., Craig D., Vogel V., and Schulten K. Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics. J. Mol. Biol. 323 5 (2002) 939-950
    • (2002) J. Mol. Biol. , vol.323 , Issue.5 , pp. 939-950
    • Gao, M.1    Craig, D.2    Vogel, V.3    Schulten, K.4
  • 19
    • 0345133287 scopus 로고    scopus 로고
    • Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
    • Garcia A., and Onuchic J. Folding a protein in a computer: An atomic description of the folding/unfolding of protein A. Proc. Natl. Acad. Sci. USA 100 24 (2003) 13898-13903
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , Issue.24 , pp. 13898-13903
    • Garcia, A.1    Onuchic, J.2
  • 20
    • 0035865992 scopus 로고    scopus 로고
    • Exploring the energy landscape of a beta hairpin in explicit solvent
    • Garcia A., and Sanbonmatsu K. Exploring the energy landscape of a beta hairpin in explicit solvent. Proteins 42 3 (2001) 345-354
    • (2001) Proteins , vol.42 , Issue.3 , pp. 345-354
    • Garcia, A.1    Sanbonmatsu, K.2
  • 22
    • 18844398202 scopus 로고    scopus 로고
    • Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations
    • Grater F., Shen J., Jiang H., Gautel M., and Grubmuller H. Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations. Biophys. J. 88 2 (2005) 790-804
    • (2005) Biophys. J. , vol.88 , Issue.2 , pp. 790-804
    • Grater, F.1    Shen, J.2    Jiang, H.3    Gautel, M.4    Grubmuller, H.5
  • 23
    • 0842267211 scopus 로고    scopus 로고
    • Kinetic determinants of high-fidelity tRNA discrimination on the ribosome
    • Gromadski K.B., and Rodnina M.V. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol. Cell 13 2 (2004) 191-200
    • (2004) Mol. Cell , vol.13 , Issue.2 , pp. 191-200
    • Gromadski, K.B.1    Rodnina, M.V.2
  • 24
    • 21344467900 scopus 로고    scopus 로고
    • Force probe molecular dynamics simulations
    • Grubmuller H. Force probe molecular dynamics simulations. Methods Mol. Biol. 305 (2005) 493-515
    • (2005) Methods Mol. Biol. , vol.305 , pp. 493-515
    • Grubmuller, H.1
  • 28
    • 0001002688 scopus 로고
    • Molecular dynamics simulation on a parallel computer
    • Heller H., Grubmuller H., and Schulten K. Molecular dynamics simulation on a parallel computer. Molecular Simulation 5 (1990) 133-165
    • (1990) Molecular Simulation , vol.5 , pp. 133-165
    • Heller, H.1    Grubmuller, H.2    Schulten, K.3
  • 29
    • 0001008704 scopus 로고
    • Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal-phases
    • Heller H., Schaefer M., and Schulten K. Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal-phases. J. Phys. Chem. 97 (1993) 8343-8360
    • (1993) J. Phys. Chem. , vol.97 , pp. 8343-8360
    • Heller, H.1    Schaefer, M.2    Schulten, K.3
  • 30
    • 33847205991 scopus 로고    scopus 로고
    • Kale, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K., and Schulten, K. .
  • 32
    • 0002479236 scopus 로고    scopus 로고
    • Charm++: parallel programming with message-driven objects
    • Wilson G.V., and Lu P. (Eds), MIT Press, Boston
    • Kale L.V., and Kirshnan S. Charm++: parallel programming with message-driven objects. In: Wilson G.V., and Lu P. (Eds). Parallel Programming using C++ (1996), MIT Press, Boston 175-213
    • (1996) Parallel Programming using C++ , pp. 175-213
    • Kale, L.V.1    Kirshnan, S.2
  • 33
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M., and McCammon J. Molecular dynamics simulations of biomolecules. Nature Structural Biology 9 9 (2002) 646-652
    • (2002) Nature Structural Biology , vol.9 , Issue.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.2
  • 34
    • 0030805890 scopus 로고    scopus 로고
    • Binding of the estrogen receptor to DNA The role of waters
    • Kosztin D., Bishop T.C., and Schulten K. Binding of the estrogen receptor to DNA The role of waters. Biophys. J. 73 2 (1997) 557-570
    • (1997) Biophys. J. , vol.73 , Issue.2 , pp. 557-570
    • Kosztin, D.1    Bishop, T.C.2    Schulten, K.3
  • 35
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing of the human genome
    • Lander E.S., et al. Initial sequencing of the human genome. Nature 409 6822 (2001) 860-921
    • (2001) Nature , vol.409 , Issue.6822 , pp. 860-921
    • Lander, E.S.1
  • 36
    • 0034665864 scopus 로고    scopus 로고
    • A dynamic model for the allosteric mechanism of GroEL
    • Ma J., Sigler P., Xu Z., and Karplus M. A dynamic model for the allosteric mechanism of GroEL. Journal of Molecular Biology 302 2 (2000) 303-313
    • (2000) Journal of Molecular Biology , vol.302 , Issue.2 , pp. 303-313
    • Ma, J.1    Sigler, P.2    Xu, Z.3    Karplus, M.4
  • 37
    • 0345098288 scopus 로고    scopus 로고
    • Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles
    • Marrink S.J., and Mark A.E. Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles. J. Am. Chem. Soc. 125 49 (2003) 15233-15242
    • (2003) J. Am. Chem. Soc. , vol.125 , Issue.49 , pp. 15233-15242
    • Marrink, S.J.1    Mark, A.E.2
  • 38
    • 0028063256 scopus 로고
    • Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics
    • Mathiowetz A.M., Jain A., Karasawa N., and Goddard III W.A. Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. Proteins 20 3 (1994) 227-247
    • (1994) Proteins , vol.20 , Issue.3 , pp. 227-247
    • Mathiowetz, A.M.1    Jain, A.2    Karasawa, N.3    Goddard III, W.A.4
  • 39
  • 41
    • 33847194137 scopus 로고    scopus 로고
    • Phillips, J. 2005. NAMD Performance. In .
  • 42
    • 33847218907 scopus 로고    scopus 로고
    • Phillips, J., Gengbin, Z., Kumar, S., and Kale, L. 2002. NAMD: biomolecular simulation on thousands of processors. Proceedings of the SuperComputing 2002 annual meeting.
  • 43
    • 0037453255 scopus 로고    scopus 로고
    • Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs
    • Sanbonmatsu K.Y., and Joseph S. Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs. J. Mol. Biol. 328 1 (2003) 33-47
    • (2003) J. Mol. Biol. , vol.328 , Issue.1 , pp. 33-47
    • Sanbonmatsu, K.Y.1    Joseph, S.2
  • 44
    • 27644502679 scopus 로고    scopus 로고
    • Simulating movement of tRNA into the ribosome during decoding
    • Sanbonmatsu K.Y., Joseph S., and Tung C.S. Simulating movement of tRNA into the ribosome during decoding. Proc. Natl. Acad. Sci. USA 102 44 (2005) 15854-15859
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , Issue.44 , pp. 15854-15859
    • Sanbonmatsu, K.Y.1    Joseph, S.2    Tung, C.S.3
  • 45
    • 0033855843 scopus 로고    scopus 로고
    • Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge
    • Sarzynska J., Kulinski T., and Nilsson L. Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge. Biophysical Journal 79 3 (2000) 1213-1227
    • (2000) Biophysical Journal , vol.79 , Issue.3 , pp. 1213-1227
    • Sarzynska, J.1    Kulinski, T.2    Nilsson, L.3
  • 46
    • 33847224417 scopus 로고    scopus 로고
    • SC03. 2004. . In Top 500 list.
  • 47
    • 0028455053 scopus 로고
    • Targeted molecular dynamics: a new approach for searching pathways of conformational transitions
    • Schlitter J., Engels M., and Kruger P. Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. J. Mol. Graph. 12 2 (1994) 84-89
    • (1994) J. Mol. Graph. , vol.12 , Issue.2 , pp. 84-89
    • Schlitter, J.1    Engels, M.2    Kruger, P.3
  • 48
    • 22144496413 scopus 로고    scopus 로고
    • Does water play a structural role in the folding of small nucleic acids?
    • Sorin E.J., Rhee Y.M., and Pande V.S. Does water play a structural role in the folding of small nucleic acids?. Biophys. J. 88 4 (2005) 2516-2524
    • (2005) Biophys. J. , vol.88 , Issue.4 , pp. 2516-2524
    • Sorin, E.J.1    Rhee, Y.M.2    Pande, V.S.3
  • 49
    • 32644451166 scopus 로고    scopus 로고
    • Molecular dynamics simulations of sarcin-ricin rRNA motif
    • Spackova N., and Sponer J. Molecular dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Res. 34 2 (2006) 697-708
    • (2006) Nucleic Acids Res. , vol.34 , Issue.2 , pp. 697-708
    • Spackova, N.1    Sponer, J.2
  • 50
    • 0037134267 scopus 로고    scopus 로고
    • Control of the selectivity of the aquaporin water channel family by global orientational tuning
    • Tajkhorshid E., Nollert P., Jensen M.O., Miercke L.J., O'Connell J., Stroud R.M., and Schulten K. Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science 296 5567 (2002) 525-530
    • (2002) Science , vol.296 , Issue.5567 , pp. 525-530
    • Tajkhorshid, E.1    Nollert, P.2    Jensen, M.O.3    Miercke, L.J.4    O'Connell, J.5    Stroud, R.M.6    Schulten, K.7
  • 51
    • 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., and Brooks C. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl. Acad. Sci. USA 100 16 (2003) 9319-9323
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , Issue.16 , pp. 9319-9323
    • Tama, F.1    Valle, M.2    Frank, J.3    Brooks, C.4
  • 52
    • 4544356700 scopus 로고    scopus 로고
    • The molecular basis of electroporation
    • Tieleman D.P. The molecular basis of electroporation. BMC Biochem. 5 (2004) 10
    • (2004) BMC Biochem. , vol.5 , pp. 10
    • Tieleman, D.P.1
  • 53
    • 24144478280 scopus 로고    scopus 로고
    • Exploring global motions and correlations in the ribosome
    • Trylska J., Tozzini V., and McCammon J.A. Exploring global motions and correlations in the ribosome. Biophys. J (2005)
    • (2005) Biophys. J
    • Trylska, J.1    Tozzini, V.2    McCammon, J.A.3
  • 54
    • 16644372753 scopus 로고    scopus 로고
    • Atomic model of the Thermus thermophilus 70S ribosome developed in silico
    • Tung C.S., and Sanbonmatsu K.Y. Atomic model of the Thermus thermophilus 70S ribosome developed in silico. Biophys. J. 87 4 (2004) 2714-2722
    • (2004) Biophys. J. , vol.87 , Issue.4 , pp. 2714-2722
    • Tung, C.S.1    Sanbonmatsu, K.Y.2
  • 57
    • 0020480264 scopus 로고
    • Protein dynamics in solution and in a crystalline environment: a molecular dynamics study
    • Van Gunsteren W., and Karplus M. Protein dynamics in solution and in a crystalline environment: a molecular dynamics study. Biochemistry 21 (1982) 2259-2274
    • (1982) Biochemistry , vol.21 , pp. 2259-2274
    • Van Gunsteren, W.1    Karplus, M.2
  • 59
    • 0035815288 scopus 로고    scopus 로고
    • Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation
    • Young M.A., Gonfloni S., Superti-Furga G., Roux B., and Kuriyan J. Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 105 (2001) 115-126
    • (2001) Cell , vol.105 , pp. 115-126
    • Young, M.A.1    Gonfloni, S.2    Superti-Furga, G.3    Roux, B.4    Kuriyan, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.