메뉴 건너뛰기




Volumn 391, Issue 3, 2012, Pages 905-916

Network analysis of transmembrane protein structures

Author keywords

Amino acids; Nodes; Small world network

Indexed keywords

AMINO ACIDS; GRAPH THEORY; SMALL-WORLD NETWORKS;

EID: 80455143537     PISSN: 03784371     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.physa.2011.08.065     Document Type: Article
Times cited : (15)

References (50)
  • 1
    • 0035826155 scopus 로고    scopus 로고
    • Exploring complex networks
    • DOI 10.1038/35065725
    • S.H. Strogatz Exploring complex networks Nature 410 2001 268 276 (Pubitemid 32216604)
    • (2001) Nature , vol.410 , Issue.6825 , pp. 268-276
    • Strogatz, S.H.1
  • 2
    • 0036008543 scopus 로고    scopus 로고
    • Scale-free networks in biology: New insights into the fundamentals of evolution?
    • DOI 10.1002/bies.10059
    • Y.I. Wolf, G. Karev, and E.V. Koonin Scale-free networks in biology: new insights into the fundamentals of evolution? Bioessays 24 2 2002 105 109 (Pubitemid 34179287)
    • (2002) BioEssays , vol.24 , Issue.2 , pp. 105-109
    • Wolf, Y.I.1    Karev, G.2    Koonin, E.V.3
  • 4
    • 0003737454 scopus 로고    scopus 로고
    • Oxford University Press New York
    • S.A. Kauffman Investigations 2000 Oxford University Press New York
    • (2000) Investigations
    • Kauffman, S.A.1
  • 7
    • 1842580761 scopus 로고    scopus 로고
    • Functional and topological characterization of protein interaction networks
    • DOI 10.1002/pmic.200300636
    • S.H. Yook, Z.N. Oltvai, and A.L. Barabasi Functional and topological characterization of protein interaction networks Proteomics 4 2004 928 942 (Pubitemid 38445953)
    • (2004) Proteomics , vol.4 , Issue.4 , pp. 928-942
    • Yook, S.-H.1    Oltvai, Z.N.2    Barabasi, A.-L.3
  • 9
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • DOI 10.1126/science.1073374
    • E. Ravasz, A.L. Somera, D.A. Mongru, Z.N. Oltvai, and A.L. Barabasi Hierarchical organization of modularity in metabolic networks Science 297 2002 1551 1555 (Pubitemid 34971002)
    • (2002) Science , vol.297 , Issue.5586 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3    Oltvai, Z.N.4    Barabasi, A.-L.5
  • 10
    • 0037686112 scopus 로고    scopus 로고
    • The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster
    • DOI 10.1016/S0022-5193(03)00035-3
    • R. Albert, and H.G. Othmer The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster J. Theoret. Biol. 223 2003 1 18 (Pubitemid 36627542)
    • (2003) Journal of Theoretical Biology , vol.223 , Issue.1 , pp. 1-18
    • Albert, R.1    Othmer, H.G.2
  • 12
    • 41349118690 scopus 로고    scopus 로고
    • Small-world view of the amino acids that play a key role in protein folding
    • M. Vendruscolo, N.V. Dokholyan, E. Paci, and M. Karplus Small-world view of the amino acids that play a key role in protein folding Phys. Rev. E 65 2002 061910
    • (2002) Phys. Rev. e , vol.65 , pp. 061910
    • Vendruscolo, M.1    Dokholyan, N.V.2    Paci, E.3    Karplus, M.4
  • 13
    • 0242720597 scopus 로고    scopus 로고
    • Uncovering network systems within protein structures
    • DOI 10.1016/j.jmb.2003.08.061
    • L.H. Greene, and V.A. Victoria Uncovering network systems with in protein structures J. Mol. Biol. 334 2003 781 791 (Pubitemid 37433891)
    • (2003) Journal of Molecular Biology , vol.334 , Issue.4 , pp. 781-791
    • Greene, L.H.1    Higman, V.A.2
  • 14
    • 0346057951 scopus 로고    scopus 로고
    • Small-World Communication of Residues and Significance for Protein Dynamics
    • A.R. Atilgan, P. Akan, and C. Baysal Small-world communication of residues and significance for protein dynamics Biophys. J. 86 2004 85 91 (Pubitemid 38067438)
    • (2004) Biophysical Journal , vol.86 , Issue.1 , pp. 85-91
    • Atilgan, A.R.1    Akan, P.2    Baysal, C.3
  • 16
    • 33748207211 scopus 로고    scopus 로고
    • Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non-enzyme families
    • DOI 10.1110/ps.062249106
    • D.S. Antonio, H. Fujihashi, D. Amoros, and R. Nussinov Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families Protein Sci. 15 2006 2120 2128 (Pubitemid 44316014)
    • (2006) Protein Science , vol.15 , Issue.9 , pp. 2120-2128
    • Del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 18
    • 34249910312 scopus 로고    scopus 로고
    • Network analysis of protein dynamics
    • DOI 10.1016/j.febslet.2007.05.021, PII S0014579307005492, Vienna Special Issue: Molecular Machines
    • C. Bode, I.A. Kovacs, M.S. Szalayb, R. Palotaib, T. Korcsmarosb, and P. Csermely Network analysis of protein dynamics FEBS Lett. 581 2007 2776 2782 (Pubitemid 46874391)
    • (2007) FEBS Letters , vol.581 , Issue.15 , pp. 2776-2782
    • Bode, C.1    Kovacs, I.A.2    Szalay, M.S.3    Palotai, R.4    Korcsmaros, T.5    Csermely, P.6
  • 19
    • 80455139382 scopus 로고    scopus 로고
    • Static and dynamic characteristics of protein contact networks
    • abs/1011.2
    • S. Khor, Static and dynamic characteristics of protein contact networks, Computing Research Repository, 2010 abs/1011.2.
    • (2010) Computing Research Repository
    • Khor, S.1
  • 20
    • 0031954925 scopus 로고    scopus 로고
    • Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
    • E. Wallin, and G.V. Heijne Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms Protein Sci. 7 1998 1029 1038 (Pubitemid 28216544)
    • (1998) Protein Science , vol.7 , Issue.4 , pp. 1029-1038
    • Wallin, E.1    Von Heijne, G.2
  • 21
    • 0033956331 scopus 로고    scopus 로고
    • Riding the wave: Structural and energetic principles of helical membrane proteins
    • DOI 10.1016/S0958-1669(99)00056-7
    • K.G. Fleming Riding the wave: structural and energetic principles of helical membrane proteins Curr. Opin. Biotechnol. 11 2000 67 71 (Pubitemid 30099041)
    • (2000) Current Opinion in Biotechnology , vol.11 , Issue.1 , pp. 67-71
    • Fleming, K.G.1
  • 22
    • 0037136435 scopus 로고    scopus 로고
    • Genomic analysis of membrane protein families: Abundance and conserved motifs
    • research0054
    • Y. Liu, D.M. Engelman, and M. Gerstein Genomic analysis of membrane protein families: abundance and conserved motifs Genome Biol. 3 2002 research0054
    • (2002) Genome Biol. , vol.3
    • Liu, Y.1    Engelman, D.M.2    Gerstein, M.3
  • 23
    • 0030274647 scopus 로고    scopus 로고
    • Genomic sciences and the medicine of tomorrow: Commentary on drug development
    • J. Drews Genomic sciences and the medicine of tomorrow: commentary on drug development Nat. Biotech. 14 1996 1516 1518
    • (1996) Nat. Biotech. , vol.14 , pp. 1516-1518
    • Drews, J.1
  • 24
    • 0037020329 scopus 로고    scopus 로고
    • Drug design strategies for targeting G-protein-coupled receptors
    • DOI 10.1002/1439-7633(20021004)3:10<928::AID-CBIC928>3.0.CO;2-5
    • T. Klabunde, and G. Hessler Drug design strategies for targeting G-protein-coupled receptors Chem. Biol. Chem. 3 2002 928 944 (Pubitemid 35189597)
    • (2002) ChemBioChem , vol.3 , Issue.10 , pp. 928-944
    • Klabunde, T.1    Hessler, G.2
  • 25
    • 0017309766 scopus 로고
    • Structural patterns in globular proteins
    • M. Levitt, and C. Chothia Structural patterns in globular proteins Nature 261 1976 552 558
    • (1976) Nature , vol.261 , pp. 552-558
    • Levitt, M.1    Chothia, C.2
  • 28
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • I. Bahar, A.R. Atilgan, and B. Erman Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential Fold Des. 2 1997 173 181 (Pubitemid 127740467)
    • (1997) Folding and Design , vol.2 , Issue.3 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 29
    • 0034622725 scopus 로고    scopus 로고
    • Identifying the adaptive mechanism in globular proteins: Fluctuations in densely packed regions manipulate flexible parts
    • L.S. Yilmaz, and A.R. Atilgan Identifying the adaptive mechanism in globular proteins: fluctuations in densely packed regions manipulate flexible parts J. Chem. Phys. 113 2000 4454 4464
    • (2000) J. Chem. Phys. , vol.113 , pp. 4454-4464
    • Yilmaz, L.S.1    Atilgan, A.R.2
  • 30
    • 10244252813 scopus 로고    scopus 로고
    • Transmembrane proteins in the Protein Data Bank: Identification and classification
    • DOI 10.1093/bioinformatics/bth340
    • G.E. Tusnady, Z. Dosztanyi, and I. Simon Transmembrane proteins in the Protein Data Bank: identification and classification Bioinformatics 20 17 2004 2964 2972 (Pubitemid 39619188)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 2964-2972
    • Tusnady, G.E.1    Dosztanyi, Z.2    Simon, I.3
  • 32
    • 34447270231 scopus 로고    scopus 로고
    • Hydrophobic, hydrophilic, and charged amino acid networks within protein
    • DOI 10.1529/biophysj.106.098004
    • M.d. Aftabuddin, and S. Kundu Hydrophobic, hydrophilic, and charged amino acid networks within protein Biophys. J. 93 2007 225 231 (Pubitemid 47041667)
    • (2007) Biophysical Journal , vol.93 , Issue.1 , pp. 225-231
    • Aftabuddin, Md.1    Kundu, S.2
  • 33
    • 0004219960 scopus 로고
    • Academic Press London, Orlando
    • B. Bollobas Random Graphs 1985 Academic Press London, Orlando
    • (1985) Random Graphs
    • Bollobas, B.1
  • 35
    • 60449097068 scopus 로고    scopus 로고
    • Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins
    • V. Pabuwal, and Z. Li Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins Protein Eng. Des. Selection 22 2009 67 73
    • (2009) Protein Eng. Des. Selection , vol.22 , pp. 67-73
    • Pabuwal, V.1    Li, Z.2
  • 36
    • 84945709831 scopus 로고
    • Algorithm 97
    • R.W. Floyd Algorithm 97 Comm. ACM 56 1962 345
    • (1962) Comm. ACM , vol.56 , pp. 345
    • Floyd, R.W.1
  • 38
    • 33750177351 scopus 로고
    • Centrality in social networks conceptual clarification
    • L. Freeman Centrality in social networks conceptual clarification Soc. Netw. 1 1979 215 239
    • (1979) Soc. Netw. , vol.1 , pp. 215-239
    • Freeman, L.1
  • 39
    • 0038449074 scopus 로고
    • An improved index of centrality
    • M.A. Beauchamp An improved index of centrality Behav. Sci. 10 1965 161 163
    • (1965) Behav. Sci. , vol.10 , pp. 161-163
    • Beauchamp, M.A.1
  • 40
    • 0013987194 scopus 로고
    • The centrality of a graph
    • G. Sabidussi The centrality of a graph Psychometrika 31 1966 581 603
    • (1966) Psychometrika , vol.31 , pp. 581-603
    • Sabidussi, G.1
  • 41
    • 18744389789 scopus 로고    scopus 로고
    • Assortative mixing in networks
    • M.E.J. Newman Assortative mixing in networks Phys. Rev. Lett. 89 2002 208701
    • (2002) Phys. Rev. Lett. , vol.89 , pp. 208701
    • Newman, M.E.J.1
  • 43
    • 41349090299 scopus 로고    scopus 로고
    • Large-scale topological and dynamical properties of the Internet
    • A. Vazquez, S.R. Pastor, and A. Vespignani Large-scale topological and dynamical properties of the Internet Phys. Rev. E 65 2002 066130
    • (2002) Phys. Rev. e , vol.65 , pp. 066130
    • Vazquez, A.1    Pastor, S.R.2    Vespignani, A.3
  • 44
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of small world networks
    • D.J. Watts, and S.H. Strogatz Collective dynamics of small world networks Nature 393 1998 440 442
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 46
    • 9944223645 scopus 로고    scopus 로고
    • Network properties of protein structures
    • G. Bagler, and S. Sinha Network properties of protein structures Physica A 346 2005 27 33
    • (2005) Physica A , vol.346 , pp. 27-33
    • Bagler, G.1    Sinha, S.2
  • 47
    • 0037370648 scopus 로고    scopus 로고
    • Hydrophobicity of transmembrane proteins: Spatially profiling the distribution
    • DOI 10.1110/ps.0214903
    • B.D. Silverman Hydrophobicity of transmembrane proteins: spatially profiling the distribution Protein Sci. 12 2003 586 599 (Pubitemid 36241115)
    • (2003) Protein Science , vol.12 , Issue.3 , pp. 586-599
    • Silverman, B.D.1
  • 48
    • 0001492480 scopus 로고
    • Centrality in valued graphs: A measure of betweenness based on network flow
    • L.C. Freeman, S.P. Borgatti, and D.R. White Centrality in valued graphs: a measure of betweenness based on network flow Social Netw. 13 1991 141 154
    • (1991) Social Netw. , vol.13 , pp. 141-154
    • Freeman, L.C.1    Borgatti, S.P.2    White, D.R.3
  • 49
    • 25944437904 scopus 로고    scopus 로고
    • Dynamical and correlation properties of internet
    • S.R. Pastor, A. Vazquez, and A. Vespignani Dynamical and correlation properties of internet Phys. Rev. Lett. 87 2001 258701
    • (2001) Phys. Rev. Lett. , vol.87 , pp. 258701
    • Pastor, S.R.1    Vazquez, A.2    Vespignani, A.3
  • 50
    • 34547909602 scopus 로고    scopus 로고
    • Assortative mixing in protein contact networks and protein folding kinetics
    • DOI 10.1093/bioinformatics/btm257
    • G. Bagler, and S. Sinha Assortative mixing in protein contact networks and protein folding kinetics Bioinformatics 23 14 2007 1760 1767 (Pubitemid 47250308)
    • (2007) Bioinformatics , vol.23 , Issue.14 , pp. 1760-1767
    • Bagler, G.1    Sinha, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.