메뉴 건너뛰기




Volumn 10, Issue 4, 2012, Pages

A chemical group graph representation for efficient high-throughput analysis of atomistic protein simulations

Author keywords

data mining; Graph; molecular dynamics; network; protein

Indexed keywords

PROTEIN;

EID: 84863680904     PISSN: 02197200     EISSN: 17576334     Source Type: Journal    
DOI: 10.1142/S0219720012500084     Document Type: Article
Times cited : (21)

References (27)
  • 4
    • 0035882545 scopus 로고    scopus 로고
    • Elucidating protein secondary structures using alpha-carbon recurrence quantifications
    • Webber CL, Giuliani A, Zbilut JP, Colosimo A, Elucidating protein secondary structures using alpha-carbon recurrence quantifications, Proteins 44(3):292-303, 2001.
    • (2001) Proteins , vol.44 , Issue.3 , pp. 292-303
    • Webber, C.L.1    Giuliani, A.2    Zbilut, J.P.3    Colosimo, A.4
  • 5
    • 41349118690 scopus 로고    scopus 로고
    • Small-world view of the amino acids that play a key role in protein folding
    • Vendruscolo M, Dokholyan NV, Paci E, Karplus M, Small-world view of the amino acids that play a key role in protein folding, Phys Rev E 65(6):061,910, 2002.
    • (2002) Phys. Rev. E , vol.65 , Issue.6 , pp. 061-910
    • Vendruscolo, M.1    Dokholyan, N.V.2    Paci, E.3    Karplus, M.4
  • 7
    • 0026686241 scopus 로고
    • Analysis of protein sheet topologies by graph theoretical methods
    • Koch I, Kaden F, Selbig J, Analysis of protein sheet topologies by graph theoretical methods, Proteins 12(4):314-323, 1992.
    • (1992) Proteins , vol.12 , Issue.4 , pp. 314-323
    • Koch, I.1    Kaden, F.2    Selbig, J.3
  • 8
    • 0028578645 scopus 로고
    • Interhelical contacts determining the architecture of alpha-helical globular proteins
    • Grigoriev IV, Mironov AA, Rakhmaninova AB, Interhelical contacts determining the architecture of alpha-helical globular proteins, J Biomol Struct Dynamics 12(3):559-572, 1994.
    • (1994) J. Biomol. Struct Dynamics , vol.12 , Issue.3 , pp. 559-572
    • Grigoriev, I.V.1    Mironov, A.A.2    Rakhmaninova, A.B.3
  • 9
    • 77953285974 scopus 로고    scopus 로고
    • Network models for molecular kinetics and their initial applications to human health
    • Bowman GR, Huang X, Pande VS, Network models for molecular kinetics and their initial applications to human health, Cell Res 20:622-630, 2010.
    • (2010) Cell Res. , vol.20 , pp. 622-630
    • Bowman, G.R.1    Huang, X.2    Pande, V.S.3
  • 15
    • 0001571646 scopus 로고
    • Surla sph-ere vide a la memoire de georges voronoi Izvestiya Akademii Nauk SSSR
    • Delaunay B, Sur la sph-ere vide. a la memoire de georges voronoi, Izvestiya Akademii Nauk SSSR, Otdelenie Matematicheskih i Estestvennyh Nauk 7:793-800, 1934.
    • (1934) Otdelenie Matematicheskih i Estestvennyh Nauk , vol.7 , pp. 793-800
    • Delaunay, B.1
  • 16
    • 0001132486 scopus 로고
    • Competitive hebbian learning rule forms perfectly topology preserving maps, in Gielen S, Kappen B (Eds.)
    • Springer Verlag, Heidelberg, Germany
    • Martinetz T, Competitive hebbian learning rule forms perfectly topology preserving maps, in Gielen S, Kappen B (Eds.), Proc Int Conf Artificial Neural Networks (ICANN- 93), Springer Verlag, Heidelberg, Germany, pp. 427-434, 1993.
    • (1993) Proc. Int. Conf. Artificial Neural Networks (ICANN- 93) , pp. 427-434
    • Martinetz, T.1
  • 17
    • 77950854473 scopus 로고    scopus 로고
    • An online approach for mining collective behaviors from molecular dynamics simulations
    • Ramanathan A, Agarwal PK, M Kurnikova, Langmead CJ, An online approach for mining collective behaviors from molecular dynamics simulations, J Comput Biol 17 (3):309-324, 2010.
    • (2010) J. Comput. Biol. , vol.17 , Issue.3 , pp. 309-324
    • Ramanathan, A.1    Agarwal, P.K.2    Kurnikova, M.3    Langmead, C.J.4
  • 18
    • 84865662866 scopus 로고    scopus 로고
    • Protein simulation data in the relational model
    • 10.1007/S11227-011-0692-3
    • Simms AM, Daggett V, Protein simulation data in the relational model, J Supercomput DOI:10.1007/S11227-011-0692-3, 2012.
    • (2012) J. Supercomput.
    • Simms, A.M.1    Daggett, V.2
  • 21
    • 0029633167 scopus 로고
    • Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
    • Levitt M, Hirshberg M, Sharon R, Daggett V, Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution, Computer Phys Commun 91(1-3):215-231, 1995.
    • (1995) Computer Phys. Commun. , vol.91 , Issue.1-3 , pp. 215-231
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Daggett, V.4
  • 22
    • 0000125216 scopus 로고    scopus 로고
    • Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution
    • Levitt M, Hirshberg M, Sharon R, Laidig K, Daggett V, Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution, J Phys Chem B 101(25):5051-5061, 1997.
    • (1997) J. Phys. Chem. B. , vol.101 , Issue.25 , pp. 5051-5061
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Laidig, K.4    Daggett, V.5
  • 23
    • 44649195146 scopus 로고    scopus 로고
    • Dynameomics: Design of a computational lab work̊ow and scientific data repository for protein simulations,Protein: Design
    • Simms AM, Toofanny RD, Kehl C, Benson NC, Daggett V, Dynameomics: Design of a computational lab work̊ow and scientific data repository for protein simulations,Protein: Design, Eng Select 21:369-377, 2008.
    • (2008) Eng. Select , vol.21 , pp. 369-377
    • Simms, A.M.1    Toofanny, R.D.2    Kehl, C.3    Benson, N.C.4    Daggett, V.5
  • 24
    • 0141524060 scopus 로고    scopus 로고
    • A consensus view of fold space: Combining scop cath, and the dali domain dictionary
    • Day R, Beck DAC, Armen RS, Daggett V, A consensus view of fold space: Combining scop, cath, and the dali domain dictionary, Protein Sci 12:2150-2160, 2003.
    • (2003) Protein Sci. , vol.12 , pp. 2150-2160
    • Day, R.1    Beck, D.A.C.2    Armen, R.S.3    Daggett, V.4
  • 25
    • 28444453011 scopus 로고    scopus 로고
    • A network representation of protein structures: Implications for pro tein stability
    • Brinda KV, Vishveshwara S, A network representation of protein structures: Implications for pro tein stability, Biophys J 89:4159-4170, 2005.
    • (2005) Biophys J. , vol.89 , pp. 4159-4170
    • Brinda, K.V.1    Vishveshwara, S.2
  • 27
    • 0004062749 scopus 로고    scopus 로고
    • 7th Edn, Wolfram Research, Inc., Champaign, Illinois
    • Wolfram Research I, Mathematica, 7th Edn, Wolfram Research, Inc., Champaign, Illinois, 2008.
    • Mathematica , pp. 2008
    • Wolfram Research, I.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.