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Volumn 46, Issue 6, 2014, Pages 1419-1439

The construction of an amino acid network for understanding protein structure and function

Author keywords

Amino acid network; Network properties; Protein structure and function; Software tools

Indexed keywords

AMINO ACID NETWORK; COMPARATIVE STUDY; COMPLEX FORMATION; COMPUTER PROGRAM; CONFORMATIONAL TRANSITION; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; REVIEW; STRUCTURE ANALYSIS; THERMOSTABILITY; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PROCEDURES; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEOMICS;

EID: 84901451274     PISSN: 09394451     EISSN: 14382199     Source Type: Journal    
DOI: 10.1007/s00726-014-1710-6     Document Type: Review
Times cited : (93)

References (127)
  • 1
    • 33645830948 scopus 로고    scopus 로고
    • CFinder: Locating cliques and overlapping modules in biological networks
    • doi:10.1093/bioinformatics/btl039
    • Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T (2006) CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22(8):1021-1023. doi:10.1093/bioinformatics/btl039
    • (2006) Bioinformatics , vol.22 , Issue.8 , pp. 1021-1023
    • Adamcsek, B.1    Palla, G.2    Farkas, I.J.3    Derenyi, I.4    Vicsek, T.5
  • 2
    • 33745684683 scopus 로고    scopus 로고
    • Weighted and unweighted network of amino acids within protein
    • doi:10.1016/j.physa.2006.03.056
    • Aftabuddin M, Kundu S (2006) Weighted and unweighted network of amino acids within protein. Phys A 369(2):895-904. doi:10.1016/j.physa.2006.03.056
    • (2006) Phys A , vol.369 , Issue.2 , pp. 895-904
    • Aftabuddin, M.1    Kundu, S.2
  • 3
    • 34447270231 scopus 로고    scopus 로고
    • Hydrophobic, hydrophilic, and charged amino acid networks within protein
    • DOI 10.1529/biophysj.106.098004
    • Aftabuddin M, Kundu S (2007) Hydrophobic, hydrophilic, and charged amino acid networks within protein. Biophys J 93(1):225-231. doi:10.1529/biophysj.106. 098004 (Pubitemid 47041667)
    • (2007) Biophysical Journal , vol.93 , Issue.1 , pp. 225-231
    • Aftabuddin, M.1    Kundu, S.2
  • 4
    • 0033117763 scopus 로고    scopus 로고
    • Matching theory and experiment in protein folding
    • doi:10.1016/S0959-440X(99)80027-X
    • Alm E, Baker D (1999) Matching theory and experiment in protein folding. Curr Opin Struct Biol 9(2):189-196. doi:10.1016/S0959-440X(99)80027-X
    • (1999) Curr Opin Struct Biol , vol.9 , Issue.2 , pp. 189-196
    • Alm, E.1    Baker, D.2
  • 5
    • 33751396631 scopus 로고    scopus 로고
    • Inferring topological features of proteins from amino acid residue networks
    • DOI 10.1016/j.physa.2006.09.014, PII S0378437106009952
    • Alves NA, Martinez AS (2007) Inferring topological features of proteins from amino acid residue networks. Phys A 375(1):336-344. doi:10.1016/j.physa. 2006.09.014 (Pubitemid 44821663)
    • (2007) Physica A: Statistical Mechanics and its Applications , vol.375 , Issue.1 , pp. 336-344
    • Alves, N.A.1    Martinez, A.S.2
  • 8
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • doi:10.1126/science.181.4096.223
    • Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181(4096):223-230. doi:10.1126/science.181.4096.223
    • (1973) Science , vol.181 , Issue.4096 , pp. 223-230
    • Anfinsen, C.B.1
  • 9
    • 79953726279 scopus 로고    scopus 로고
    • Conserved amino acids participate in the structure networks deputed to intramolecular communication in the lutropin receptor
    • doi:10.1007/s00018-010-0519-z
    • Angelova K, Felline A, Lee M, Patel M, Puett D, Fanelli F (2011) Conserved amino acids participate in the structure networks deputed to intramolecular communication in the lutropin receptor. Cell Mol Life Sci 68(7):1227-1239. doi:10.1007/s00018-010-0519-z
    • (2011) Cell Mol Life Sci , vol.68 , Issue.7 , pp. 1227-1239
    • Angelova, K.1    Felline, A.2    Lee, M.3    Patel, M.4    Puett, D.5    Fanelli, F.6
  • 10
    • 38349164409 scopus 로고    scopus 로고
    • Computing topological parameters of biological networks
    • doi:10.1093/bioinfor matics/btm554
    • Assenov Y, Ramirez F, Schelhorn SE, Lengauer T, Albrecht M (2008) Computing topological parameters of biological networks. Bioinformatics 24(2):282-284. doi:10.1093/bioinfor matics/btm554
    • (2008) Bioinformatics , vol.24 , Issue.2 , pp. 282-284
    • Assenov, Y.1    Ramirez, F.2    Schelhorn, S.E.3    Lengauer, T.4    Albrecht, M.5
  • 11
    • 0346057951 scopus 로고    scopus 로고
    • Small-World Communication of Residues and Significance for Protein Dynamics
    • Atilgan AR, Akan P, Baysal C (2004) Small-world communication of residues and significance for protein dynamics. Biophys J 86(1 Pt 1):85-91. doi:10.1016/S0006-3495(04)74086-2 (Pubitemid 38067438)
    • (2004) Biophysical Journal , vol.86 , Issue.1 I , pp. 85-91
    • Atilgan, A.R.1    Akan, P.2    Baysal, C.3
  • 12
    • 34247580211 scopus 로고    scopus 로고
    • Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication
    • DOI 10.1529/biophysj.106.099440
    • Atilgan AR, Turgut D, Atilgan C (2007) Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication. Biophys J 92(9):3052-3062. doi:10.1529/biophysj.106.099440 (Pubitemid 46684566)
    • (2007) Biophysical Journal , vol.92 , Issue.9 , pp. 3052-3062
    • Atilgan, A.R.1    Turgut, D.2    Atilgan, C.3
  • 13
    • 9944223645 scopus 로고    scopus 로고
    • Network properties of protein structures
    • doi:10.1016/j.physa.2004.08.046
    • Bagler G, Sinha S (2005) Network properties of protein structures. Phys A Stat Mech Appl 346(1-2):27-33. doi:10.1016/j.physa.2004.08.046
    • (2005) Phys A Stat Mech Appl , vol.346 , Issue.1-2 , pp. 27-33
    • Bagler, G.1    Sinha, S.2
  • 14
    • 34547909602 scopus 로고    scopus 로고
    • Assortative mixing in protein contact networks and protein folding kinetics
    • DOI 10.1093/bioinformatics/btm257
    • Bagler G, Sinha S (2007) Assortative mixing in protein contact networks and protein folding kinetics. Bioinformatics 23(14):1760-1767. doi:10.1093/bioinformatics/btm257 (Pubitemid 47250308)
    • (2007) Bioinformatics , vol.23 , Issue.14 , pp. 1760-1767
    • Bagler, G.1    Sinha, S.2
  • 15
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • doi:10.1126/science.286.5439.509
    • Barabási A-L, Albert R (1999) Emergence of scaling in random networks. Science 286(5439):509-512. doi:10.1126/science.286.5439.509
    • (1999) Science , vol.286 , Issue.5439 , pp. 509-512
    • Barabási, A.-L.1    Albert, R.2
  • 16
    • 38049119840 scopus 로고    scopus 로고
    • The effect of backbone on the small-world properties of protein contact maps
    • doi:10.1088/1478-3975/4/4/L01
    • Bartoli L, Fariselli P, Casadio R (2007) The effect of backbone on the small-world properties of protein contact maps. Phys Biol 4(4):L1-L5. doi:10.1088/1478-3975/4/4/L01
    • (2007) Phys Biol , vol.4 , Issue.4
    • Bartoli, L.1    Fariselli, P.2    Casadio, R.3
  • 18
    • 84892909797 scopus 로고    scopus 로고
    • An automated approach to network features of protein structure ensembles
    • doi:10.1002/pro.2333
    • Bhattacharyya M, Bhat CR, Vishveshwara S (2013) An automated approach to network features of protein structure ensembles. Protein Sci 22(10):1399-1416. doi:10.1002/pro.2333
    • (2013) Protein Sci , vol.22 , Issue.10 , pp. 1399-1416
    • Bhattacharyya, M.1    Bhat, C.R.2    Vishveshwara, S.3
  • 19
    • 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
    • Bode C, Kovacs IA, Szalay MS, Palotai R, Korcsmaros T, Csermely P (2007) Network analysis of protein dynamics. FEBS Lett 581(15):2776-2782. doi:10.1016/j.febslet.2007.05.021 (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
  • 21
    • 28444453011 scopus 로고    scopus 로고
    • A network representation of protein structures: Implications for protein stability
    • DOI 10.1529/biophysj.105.064485
    • Brinda KV, Vishveshwara S (2005) A network representation of protein structures: implications for protein stability. Biophys J 89(6):4159-4170. doi:10.1529/biophysj.105.064485 (Pubitemid 41725636)
    • (2005) Biophysical Journal , vol.89 , Issue.6 , pp. 4159-4170
    • Brinda, K.V.1    Vishveshwara, S.2
  • 22
    • 0036093538 scopus 로고    scopus 로고
    • Analysis of homodimeric protein interfaces by graph-spectral methods
    • Brinda KV, Kannan N, Vishveshwara S (2002) Analysis of homodimeric protein interfaces by graph-spectral methods. Protein Eng 15(4):265-277. doi:10.1093/protein/15.4.265 (Pubitemid 34532765)
    • (2002) Protein Engineering , vol.15 , Issue.4 , pp. 265-277
    • Brinda, K.V.1    Kannan, N.2    Vishveshwara, S.3
  • 23
    • 26844503957 scopus 로고    scopus 로고
    • Insights into the quaternary association of proteins through structure graphs: A case study of lectins
    • DOI 10.1042/BJ20050434
    • Brinda KV, Surolia A, Vishveshwara S (2005) Insights into the quaternary association of proteins through structure graphs: a case study of lectins. Biochem J 391(Pt 1):1-15. doi:10.1042/BJ20050434 (Pubitemid 41445470)
    • (2005) Biochemical Journal , vol.391 , Issue.1 , pp. 1-15
    • Brinda, K.V.1    Surolia, A.2    Vishveshwara, S.3
  • 24
    • 41449100252 scopus 로고    scopus 로고
    • Amino acid network and its scoring application in protein- protein docking
    • doi:10.1016/j.bpc.2007.12.005
    • Chang S, Jiao X, Li CH, Gong XQ, Chen WZ, Wang CX (2008) Amino acid network and its scoring application in protein- protein docking. Biophys Chem 134(3):111-118. doi:10.1016/j.bpc.2007.12.005
    • (2008) Biophys Chem , vol.134 , Issue.3 , pp. 111-118
    • Chang, S.1    Jiao, X.2    Li, C.H.3    Gong, X.Q.4    Chen, W.Z.5    Wang, C.X.6
  • 25
    • 84863883496 scopus 로고    scopus 로고
    • Network properties of protein-decoy structures
    • doi:10.1080/07391102.2011.672625
    • Chatterjee S, Bhattacharyya M, Vishveshwara S (2012) Network properties of protein-decoy structures. J Biomol Struct Dyn 29(6):606-622. doi:10.1080/07391102.2011.672625
    • (2012) J Biomol Struct Dyn , vol.29 , Issue.6 , pp. 606-622
    • Chatterjee, S.1    Bhattacharyya, M.2    Vishveshwara, S.3
  • 26
    • 84880021080 scopus 로고    scopus 로고
    • Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis
    • doi:10.1186/1479-5876-11-169
    • Chen J, Zhang D, Zhang W, Tang Y, Yan W, Guo L, Shen B (2013) Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis. J Transl Med 11:169. doi:10.1186/1479-5876- 11-169
    • (2013) J Transl Med , vol.11 , pp. 169
    • Chen, J.1    Zhang, D.2    Zhang, W.3    Tang, Y.4    Yan, W.5    Guo, L.6    Shen, B.7
  • 27
    • 79953890453 scopus 로고    scopus 로고
    • Yeast network and report of new stochastic-credibility cell cycle models
    • Chis O, Dumitru O, Concu R, Shen B (2011) Yeast network and report of new stochastic-credibility cell cycle models. Curr Bioinform 6(1):35-43
    • (2011) Curr Bioinform , vol.6 , Issue.1 , pp. 35-43
    • Chis, O.1    Dumitru, O.2    Concu, R.3    Shen, B.4
  • 29
    • 43349094507 scopus 로고    scopus 로고
    • The igraph software package for complex network research
    • Csardi G, Nepusz T (2006) The igraph software package for complex network research. InterJ Complex Syst 1695
    • (2006) InterJ Complex Syst , vol.1695
    • Csardi, G.1    Nepusz, T.2
  • 30
    • 56449125182 scopus 로고    scopus 로고
    • Creative elements: Network-based predictions of active centres in proteins and cellular and social networks
    • doi:10.1016/j.tibs.2008.09.006
    • Csermely P (2008) Creative elements: network-based predictions of active centres in proteins and cellular and social networks. Trends Biochem Sci 33(12):569-576. doi:10.1016/j.tibs.2008.09.006
    • (2008) Trends Biochem Sci , vol.33 , Issue.12 , pp. 569-576
    • Csermely, P.1
  • 31
    • 84857131975 scopus 로고    scopus 로고
    • Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: Hypotheses and a comprehensive review
    • Csermely P, Sandhu KS, Hazai E, Hoksza Z, Kiss HJ, Miozzo F, Veres DV, Piazza F, Nussinov R (2012) Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review. Curr Protein Pept Sci 13(1):19-33
    • (2012) Curr Protein Pept Sci , vol.13 , Issue.1 , pp. 19-33
    • Csermely, P.1    Sandhu, K.S.2    Hazai, E.3    Hoksza, Z.4    Kiss, H.J.5    Miozzo, F.6    Veres, D.V.7    Piazza, F.8    Nussinov, R.9
  • 32
    • 55849106575 scopus 로고    scopus 로고
    • Efficient identification of critical residues based only on protein structure by network analysis
    • doi:10.1371/journal.pone.0000421
    • Cusack MP, Thibert B, Bredesen DE, Del Rio G (2007) Efficient identification of critical residues based only on protein structure by network analysis. PLoS ONE 2(5):e421. doi:10.1371/journal.pone.0000421
    • (2007) PLoS ONE , vol.2 , Issue.5
    • Cusack, M.P.1    Thibert, B.2    Bredesen, D.E.3    Del Rio, G.4
  • 34
    • 70350031205 scopus 로고    scopus 로고
    • Understanding protein structure from a percolation perspective
    • doi:10.1016/j.bpj.2009.07.016
    • Deb D, Vishveshwara S (2009) Understanding protein structure from a percolation perspective. Biophys J 97(6):1787-1794. doi:10.1016/j.bpj.2009.07. 016
    • (2009) Biophys J , vol.97 , Issue.6 , pp. 1787-1794
    • Deb, D.1    Vishveshwara, S.2
  • 35
    • 12944331889 scopus 로고    scopus 로고
    • Small-world network approach to identify key residues in protein-protein interaction
    • doi:10.1002/prot.20348
    • del Sol A, O'Meara P (2005) Small-world network approach to identify key residues in protein-protein interaction. Proteins 58(3):672-682. doi:10.1002/prot.20348
    • (2005) Proteins , vol.58 , Issue.3 , pp. 672-682
    • Del Sol, A.1    O'Meara, P.2
  • 36
    • 17444396776 scopus 로고    scopus 로고
    • Topology of small-world networks of protein-protein complex structures
    • DOI 10.1093/bioinformatics/bti167
    • del Sol A, Fujihashi H, O'Meara P (2005) Topology of small-world networks of protein-protein complex structures. Bioinformatics 21(8):1311-1315. doi:10.1093/bioinformatics/bti167 (Pubitemid 40542679)
    • (2005) Bioinformatics , vol.21 , Issue.8 , pp. 1311-1315
    • Del, S.A.1    Fujihashi, H.2    O'Meara, P.3
  • 37
    • 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
    • del Sol A, Fujihashi H, Amoros D, Nussinov R (2006) Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Sci 15(9):2120-2128. doi:10.1110/ps.062249106 (Pubitemid 44316014)
    • (2006) Protein Science , vol.15 , Issue.9 , pp. 2120-2128
    • Del, S.A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 38
    • 18144393488 scopus 로고    scopus 로고
    • Clique percolation in random networks
    • Derenyi I, Palla G, Vicsek T (2005) Clique percolation in random networks. Phys Rev Lett 94(16):160202
    • (2005) Phys Rev Lett , vol.94 , Issue.16 , pp. 160202
    • Derenyi, I.1    Palla, G.2    Vicsek, T.3
  • 39
    • 84875170915 scopus 로고    scopus 로고
    • Protein contact networks: An emerging paradigm in chemistry
    • doi:10.1021/cr3002356
    • Di Paola L, De Ruvo M, Paci P, Santoni D, Giuliani A (2013) Protein contact networks: an emerging paradigm in chemistry. Chem Rev 113(3):1598-1613. doi:10.1021/cr3002356
    • (2013) Chem Rev , vol.113 , Issue.3 , pp. 1598-1613
    • Di Paola, L.1    De Ruvo, M.2    Paci, P.3    Santoni, D.4    Giuliani, A.5
  • 41
    • 79954415213 scopus 로고    scopus 로고
    • Analyzing and visualizing residue networks of protein structures
    • doi:10.1016/j.tibs.2011.01.002
    • Doncheva NT, Klein K, Domingues FS, Albrecht M (2011) Analyzing and visualizing residue networks of protein structures. Trends Biochem Sci 36(4):179-182. doi:10.1016/j.tibs.2011.01.002
    • (2011) Trends Biochem Sci , vol.36 , Issue.4 , pp. 179-182
    • Doncheva, N.T.1    Klein, K.2    Domingues, F.S.3    Albrecht, M.4
  • 42
    • 84861779036 scopus 로고    scopus 로고
    • Topological analysis and interactive visualization of biological networks and protein structures
    • doi:10.1038/nprot.2012.004
    • Doncheva NT, Assenov Y, Domingues FS, Albrecht M (2012) Topological analysis and interactive visualization of biological networks and protein structures. Nat Protoc 7(4):670-685. doi:10.1038/nprot.2012.004
    • (2012) Nat Protoc , vol.7 , Issue.4 , pp. 670-685
    • Doncheva, N.T.1    Assenov, Y.2    Domingues, F.S.3    Albrecht, M.4
  • 43
    • 84869418186 scopus 로고    scopus 로고
    • NetworkView: 3D display and analysis of protein.RNA interaction networks
    • doi:10.1093/bioinformatics/bts546
    • Eargle J, LutheySchulten Z (2012) NetworkView: 3D display and analysis of protein.RNA interaction networks. Bioinformatics 28(22):3000-3001. doi:10.1093/bioinformatics/bts546
    • (2012) Bioinformatics , vol.28 , Issue.22 , pp. 3000-3001
    • Eargle, J.L.Z.1
  • 44
    • 77749318502 scopus 로고    scopus 로고
    • Universality in protein residue networks
    • doi:10.1016/j.bpj.2009.11.017
    • Estrada E (2010) Universality in protein residue networks. Biophys J 98(5):890-900. doi:10.1016/j.bpj.2009.11.017
    • (2010) Biophys J , vol.98 , Issue.5 , pp. 890-900
    • Estrada, E.1
  • 45
    • 0033204106 scopus 로고    scopus 로고
    • On power-law relationships of the Internet topology
    • DOI 10.1145/316194.316229
    • Faloutsos M, Faloutsos P, Faloutsos C (1999) On power-law relationships of the Internet topology. SIGCOMM Comput Commun Rev 29(4):251-262. doi:10.1145/316194.316229 (Pubitemid 32081870)
    • (1999) Computer Communication Review , vol.29 , Issue.4 , pp. 251-262
    • Faloutsos, M.1    Faloutsos, P.2    Faloutsos, C.3
  • 46
    • 77956626759 scopus 로고    scopus 로고
    • Structural insights into retinitis pigmentosa from unfolding simulations of rhodopsin mutants
    • doi:10.1096/fj.09-151084
    • Fanelli F, Seeber M (2010) Structural insights into retinitis pigmentosa from unfolding simulations of rhodopsin mutants. FASEB J 24(9):3196-3209. doi:10.1096/fj.09-151084
    • (2010) FASEB J , vol.24 , Issue.9 , pp. 3196-3209
    • Fanelli, F.1    Seeber, M.2
  • 48
    • 35648944297 scopus 로고    scopus 로고
    • A study of communication pathways in methionyl-tRNA synthetase by molecular dynamics simulations and structure network analysis
    • DOI 10.1073/pnas.0704459104
    • Ghosh A, Vishveshwara S (2007) A study of communication pathways in methionyl-tRNA synthetase by molecular dynamics simulations and structure network analysis. Proc Natl Acad Sci USA 104(40):15711-15716. doi:10.1073/pnas.0704459104 (Pubitemid 350035365)
    • (2007) Proceedings of the National Academy of Sciences of the United States of America , vol.104 , Issue.40 , pp. 15711-15716
    • Ghosh, A.1    Vishveshwara, S.2
  • 49
    • 55249123363 scopus 로고    scopus 로고
    • Variations in clique and community patterns in protein structures during allosteric communication: Investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes
    • doi:10.1021/bi8007559
    • Ghosh A, Vishveshwara S (2008) Variations in clique and community patterns in protein structures during allosteric communication: investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes. Biochemistry 47(44):11398-11407. doi:10.1021/bi8007559
    • (2008) Biochemistry , vol.47 , Issue.44 , pp. 11398-11407
    • Ghosh, A.1    Vishveshwara, S.2
  • 50
    • 34047195261 scopus 로고    scopus 로고
    • Dynamics of lysozyme structure network: Probing the process of unfolding
    • DOI 10.1529/biophysj.106.099903
    • Ghosh A, Brinda KV, Vishveshwara S (2007) Dynamics of lysozyme structure network: probing the process of unfolding. Biophys J 92(7):2523-2535. doi:10.1529/biophysj.106.099903 (Pubitemid 46536434)
    • (2007) Biophysical Journal , vol.92 , Issue.7 , pp. 2523-2535
    • Ghosh, A.1    Brinda, K.V.2    Vishveshwara, S.3
  • 52
    • 0020972782 scopus 로고
    • Theoretical studies of protein folding
    • doi:10.1146/annurev.bb.12.060183.001151
    • Go N (1983) Theoretical studies of protein folding. Annu Rev Biophys Bioeng 12:183-210. doi:10.1146/annurev.bb.12.060183.001151
    • (1983) Annu Rev Biophys Bioeng , vol.12 , pp. 183-210
    • Go, N.1
  • 53
    • 84870336885 scopus 로고    scopus 로고
    • Protein structure networks
    • doi:10.1093/bfgp/els039
    • Greene LH (2012) Protein structure networks. Brief Funct Genomics 11(6):469-478. doi:10.1093/bfgp/els039
    • (2012) Brief Funct Genomics , vol.11 , Issue.6 , pp. 469-478
    • Greene, L.H.1
  • 54
    • 0242720597 scopus 로고    scopus 로고
    • Uncovering network systems within protein structures
    • DOI 10.1016/j.jmb.2003.08.061
    • Greene LH, Higman VA (2003) Uncovering network systems within protein structures. J Mol Biol 334(4):781-791. doi:10.1016/j.jmb.2003.08.061 (Pubitemid 37433891)
    • (2003) Journal of Molecular Biology , vol.334 , Issue.4 , pp. 781-791
    • Greene, L.H.1    Higman, V.A.2
  • 56
    • 45349097076 scopus 로고    scopus 로고
    • statnet: Software tools for the representation, visualization, analysis and simulation of network data
    • Handcock MS, Hunter DR, Butts CT, Goodreau SM, Morris M (2008) statnet: software tools for the representation, visualization, analysis and simulation of network data. J Stat Softw 24(1):1548-7660
    • (2008) J Stat Softw , vol.24 , Issue.1 , pp. 1548-7660
    • Handcock, M.S.1    Hunter, D.R.2    Butts, C.T.3    Goodreau, S.M.4    Morris, M.5
  • 57
    • 72949085966 scopus 로고    scopus 로고
    • Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks
    • doi:10.1039/b903807h
    • Hansia P, Ghosh A, Vishveshwara S (2009) Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks. Mol BioSyst 5(12):1860-1872. doi:10.1039/b903807h
    • (2009) Mol BioSyst , vol.5 , Issue.12 , pp. 1860-1872
    • Hansia, P.1    Ghosh, A.2    Vishveshwara, S.3
  • 58
    • 84878586070 scopus 로고    scopus 로고
    • Potential application of network descriptions for understanding conformational changes and protonation states of ABC transporters
    • Hegedus T, Gyimesi G, Gaspar ME, Szalay KZ, Gangal R, Csermely P (2013) Potential application of network descriptions for understanding conformational changes and protonation states of ABC transporters. Curr Pharm Des 19(23):4155-4172
    • (2013) Curr Pharm des , vol.19 , Issue.23 , pp. 4155-4172
    • Hegedus, T.1    Gyimesi, G.2    Gaspar, M.E.3    Szalay, K.Z.4    Gangal, R.5    Csermely, P.6
  • 59
    • 0026519315 scopus 로고
    • A lattice model for protein structure prediction at low resolution
    • Hinds DA, Levitt M (1992) A lattice model for protein structure prediction at low resolution. Proc Natl Acad Sci USA 89(7):2536-2540
    • (1992) Proc Natl Acad Sci USA , vol.89 , Issue.7 , pp. 2536-2540
    • Hinds, D.A.1    Levitt, M.2
  • 60
    • 84878604130 scopus 로고    scopus 로고
    • The topology and dynamics of protein complexes: Insights from intra-molecular network theory
    • Hu G, Zhou J, Yan W, Chen J, Shen B (2013) The topology and dynamics of protein complexes: insights from intra-molecular network theory. Curr Protein Pept Sci 14(2):121-132
    • (2013) Curr Protein Pept Sci , vol.14 , Issue.2 , pp. 121-132
    • Hu, G.1    Zhou, J.2    Yan, W.3    Chen, J.4    Shen, B.5
  • 61
    • 84896335283 scopus 로고    scopus 로고
    • Residue interaction network analysis of Dronpa and a DNA clamp
    • doi:10.1016/j.jtbi.2014.01.023
    • Hu G, Yan W, Zhou J, Shen B (2014) Residue interaction network analysis of Dronpa and a DNA clamp. J Theor Biol. doi:10.1016/j.jtbi.2014.01.023
    • (2014) J Theor Biol
    • Hu, G.1    Yan, W.2    Zhou, J.3    Shen, B.4
  • 62
    • 48549099988 scopus 로고    scopus 로고
    • New amino acid indices based on residue network topology
    • 9781860949920-0015 [pii]
    • Huang J, Kawashima S, Kanehisa M (2007) New amino acid indices based on residue network topology. Genome Inform 18:152-161 (9781860949920-0015 [pii])
    • (2007) Genome Inform , vol.18 , pp. 152-161
    • Huang, J.1    Kawashima, S.2    Kanehisa, M.3
  • 64
    • 0032438190 scopus 로고    scopus 로고
    • The stability of proteins in extreme environments
    • doi:10.1016/S0959-440X(98)80094-810.1016/S0959-44
    • Jaenicke R, Bohm G (1998) The stability of proteins in extreme environments. Curr Opin Struct Biol 8(6):738-748. doi:10.1016/S0959-440X(98) 80094-810.1016/S0959-44
    • (1998) Curr Opin Struct Biol , vol.8 , Issue.6 , pp. 738-748
    • Jaenicke, R.1    Bohm, G.2
  • 65
    • 84055221808 scopus 로고    scopus 로고
    • Scoring function based on weighted residue network
    • doi:10.3390/ijms12128773
    • Jiao X, Chang S (2011) Scoring function based on weighted residue network. Int J Mol Sci 12(12):8773-8786. doi:10.3390/ijms12128773
    • (2011) Int J Mol Sci , vol.12 , Issue.12 , pp. 8773-8786
    • Jiao, X.1    Chang, S.2
  • 66
    • 34248185088 scopus 로고    scopus 로고
    • Construction and application of the weighted amino acid network based on energy
    • doi:10.1103/PhysRevE.75.051903
    • Jiao X, Chang S, Li CH, Chen WZ, Wang CX (2007) Construction and application of the weighted amino acid network based on energy. Phys Rev E Stat Nonlin Soft Matter Phys 75(5 Pt 1):051903. doi:10.1103/PhysRevE.75.051903
    • (2007) Phys Rev E Stat Nonlin Soft Matter Phys , vol.75 , Issue.5 PART 1 , pp. 051903
    • Jiao, X.1    Chang, S.2    Li, C.H.3    Chen, W.Z.4    Wang, C.X.5
  • 67
    • 11344269939 scopus 로고    scopus 로고
    • Topological determinants of protein unfolding rates
    • DOI 10.1002/prot.20324
    • Jung J, Lee J, Moon HT (2005) Topological determinants of protein unfolding rates. Proteins 58(2):389-395. doi:10.1002/prot.20324 (Pubitemid 40076052)
    • (2005) Proteins: Structure, Function and Genetics , vol.58 , Issue.2 , pp. 389-395
    • Jung, J.1    Lee, J.2    Moon, H.-T.3
  • 69
    • 0033578690 scopus 로고    scopus 로고
    • Identification of side-chain clusters in protein structures by a graph spectral method
    • DOI 10.1006/jmbi.1999.3058
    • Kannan N, Vishveshwara S (1999) Identification of side-chain clusters in protein structures by a graph spectral method. J Mol Biol 292(2):441-464. doi:10.1006/jmbi.1999.3058 (Pubitemid 29435778)
    • (1999) Journal of Molecular Biology , vol.292 , Issue.2 , pp. 441-464
    • Kannan, N.1    Vishveshwara, S.2
  • 70
    • 0034495733 scopus 로고    scopus 로고
    • Aromatic clusters: A determinant of thermal stability of thermophilic proteins
    • Kannan N, Vishveshwara S (2000) Aromatic clusters: a determinant of thermal stability of thermophilic proteins. Protein Eng 13(11):753-761. doi:10.1093/protein/13.11.753 (Pubitemid 32127573)
    • (2000) Protein Engineering , vol.13 , Issue.11 , pp. 753-761
    • Kannan, N.1    Vishveshwara, S.2
  • 71
    • 0035104601 scopus 로고    scopus 로고
    • Stabilizing interactions in the dimer interface of alpha-subunit in Escherichia coli RNA polymerase: A graph spectral and point mutation study
    • DOI 10.1110/ps.26201
    • Kannan N, Chander P, Ghosh P, Vishveshwara S, Chatterji D (2001) Stabilizing interactions in the dimer interface of alpha-subunit in Escherichia coli RNA polymerase: a graph spectral and point mutation study. Protein Sci 10(1):46-54. doi:10.1110/ps.26201 (Pubitemid 32221163)
    • (2001) Protein Science , vol.10 , Issue.1 , pp. 46-54
    • Kannan, N.1    Chander, P.2    Ghosh, P.3    Vishveshwara, S.4    Chatterji, D.5
  • 72
    • 84856888670 scopus 로고    scopus 로고
    • Discrimination of native folds using network properties of protein structures
    • Paper presented at the
    • Küçükural A, Sezerman OU, Ercil A (2008) Discrimination of native folds using network properties of protein structures. In: Paper presented at the APBC
    • (2008) APBC
    • Küçükural, A.1    Sezerman, O.U.2    Ercil, A.3
  • 73
    • 0031614960 scopus 로고    scopus 로고
    • Proteins from hyperthermophiles: Stability and enzymatic catalysis close to the boiling point of water
    • doi:10.1007/BFb0102289
    • Ladenstein R, Antranikian G (1998) Proteins from hyperthermophiles: stability and enzymatic catalysis close to the boiling point of water. Adv Biochem Eng Biotechnol 61:37-85. doi:10.1007/BFb0102289
    • (1998) Adv Biochem Eng Biotechnol , vol.61 , pp. 37-85
    • Ladenstein, R.1    Antranikian, G.2
  • 74
    • 79953186069 scopus 로고    scopus 로고
    • Novel feature for catalytic protein residues reflecting interactions with other residues
    • doi:10.1371/journal.pone.0016932
    • Li Y, Li G, Wen Z, Yin H, Hu M, Xiao J, Li M (2011a) Novel feature for catalytic protein residues reflecting interactions with other residues. PLoS ONE 6(3):e16932. doi:10.1371/journal.pone.0016932
    • (2011) PLoS ONE , vol.6 , Issue.3
    • Li, Y.1    Li, G.2    Wen, Z.3    Yin, H.4    Hu, M.5    Xiao, J.6    Li, M.7
  • 75
    • 78651230959 scopus 로고    scopus 로고
    • Predicting disease-associated substitution of a single amino acid by analyzing residue interactions
    • doi:10.1186/1471-2105-12-14
    • Li Y, Wen Z, Xiao J, Yin H, Yu L, Yang L, Li M (2011b) Predicting disease-associated substitution of a single amino acid by analyzing residue interactions. BMC Bioinform 12:14. doi:10.1186/1471-2105-12-14
    • (2011) BMC Bioinform , vol.12 , pp. 14
    • Li, Y.1    Wen, Z.2    Xiao, J.3    Yin, H.4    Yu, L.5    Yang, L.6    Li, M.7
  • 76
    • 0037316239 scopus 로고    scopus 로고
    • Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
    • DOI 10.1093/bioinformatics/19.2.270
    • Ma H, Zeng AP (2003) Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19(2):270-277. doi:10.1093/bioinformatics/19.2.270 (Pubitemid 36181913)
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 270-277
    • Ma, H.1    Zeng, A.-P.2
  • 78
    • 79960149420 scopus 로고    scopus 로고
    • RING: Networking interacting residues, evolutionary information and energetics in protein structures
    • doi:10.1093/bioinformatics/btr191
    • Martin AJ, Vidotto M, Boscariol F, Di Domenico T, Walsh I, Tosatto SC (2011) RING: networking interacting residues, evolutionary information and energetics in protein structures. Bioinformatics 27(14):2003-2005. doi:10.1093/bioinformatics/btr191
    • (2011) Bioinformatics , vol.27 , Issue.14 , pp. 2003-2005
    • Martin, A.J.1    Vidotto, M.2    Boscariol, F.3    Di Domenico, T.4    Walsh, I.5    Tosatto, S.C.6
  • 79
    • 0024972502 scopus 로고
    • Substantial increase of protein stability by multiple disulphide bonds
    • doi:10.1038/342291a0
    • Matsumura M, Signor G, Matthews BW (1989) Substantial increase of protein stability by multiple disulphide bonds. Nature 342(6247):291-293. doi:10.1038/342291a0
    • (1989) Nature , vol.342 , Issue.6247 , pp. 291-293
    • Matsumura, M.1    Signor, G.2    Matthews, B.W.3
  • 80
    • 62749124373 scopus 로고    scopus 로고
    • Residue network in protein native structure belongs to the universality class of a three-dimensional critical percolation cluster
    • doi:10.1103/PhysRevE.79.020901
    • Morita H, Takano M (2009) Residue network in protein native structure belongs to the universality class of a three-dimensional critical percolation cluster. Phys Rev E Stat Nonlin Soft Matter Phys 79(2 Pt 1):020901. doi:10.1103/PhysRevE.79.020901
    • (2009) Phys Rev E Stat Nonlin Soft Matter Phys , vol.79 , Issue.2 PART 1 , pp. 020901
    • Morita, H.1    Takano, M.2
  • 81
    • 77955411868 scopus 로고    scopus 로고
    • Computational tools for the interactive exploration of proteomic and structural data
    • doi:10.1074/mcp.R000007-MCP201
    • Morris JH, Meng EC, Ferrin TE (2010) Computational tools for the interactive exploration of proteomic and structural data. Mol Cell Proteomics 9(8):1703-1715. doi:10.1074/mcp.R000007-MCP201
    • (2010) Mol Cell Proteomics , vol.9 , Issue.8 , pp. 1703-1715
    • Morris, J.H.1    Meng, E.C.2    Ferrin, T.E.3
  • 82
    • 84858061976 scopus 로고    scopus 로고
    • JGromacs: A Java package for analyzing protein simulations
    • doi:10.1021/ci200289s
    • Munz M, Biggin PC (2012) JGromacs: a Java package for analyzing protein simulations. J Chem Inf Model 52(1):255-259. doi:10.1021/ci200289s
    • (2012) J Chem Inf Model , vol.52 , Issue.1 , pp. 255-259
    • Munz, M.1    Biggin, P.C.2
  • 83
    • 33745698176 scopus 로고    scopus 로고
    • A simple approach for protein structure discrimination based on the network pattern of conserved hydrophobic residues
    • doi:10.1093/protein/gzl009
    • Muppirala UK, Li Z (2006) A simple approach for protein structure discrimination based on the network pattern of conserved hydrophobic residues. Protein Eng Des Sel 19(6):265-275. doi:10.1093/protein/gzl009
    • (2006) Protein Eng des Sel , vol.19 , Issue.6 , pp. 265-275
    • Muppirala, U.K.1    Li, Z.2
  • 84
    • 18744389789 scopus 로고    scopus 로고
    • Assortative mixing in networks
    • doi:10.1103/PhysRevLett.89.208701
    • Newman ME (2002) Assortative mixing in networks. Phys Rev Lett 89(20):208701. doi:10.1103/PhysRevLett.89.208701
    • (2002) Phys Rev Lett , vol.89 , Issue.20 , pp. 208701
    • Newman, M.E.1
  • 86
    • 77953537026 scopus 로고    scopus 로고
    • Node centrality in weighted networks: Generalizing degree and shortest paths
    • doi:10.1016/j.socnet.2010.03.006
    • Opsahl T, Agneessens F, Skvoretz J (2010) Node centrality in weighted networks: generalizing degree and shortest paths. Soc Netw 32(3):245-251. doi:10.1016/j.socnet.2010.03.006
    • (2010) Soc Netw , vol.32 , Issue.3 , pp. 245-251
    • Opsahl, T.1    Agneessens, F.2    Skvoretz, J.3
  • 87
    • 38349175417 scopus 로고    scopus 로고
    • Network pattern of residue packing in helical membrane proteins and its application in membrane protein structure prediction
    • doi:10.1093/protein/gzm059
    • Pabuwal V, Li Z (2008) Network pattern of residue packing in helical membrane proteins and its application in membrane protein structure prediction. Protein Eng Des Sel 21(1):55-64. doi:10.1093/protein/gzm059
    • (2008) Protein Eng des Sel , vol.21 , Issue.1 , pp. 55-64
    • Pabuwal, V.1    Li, Z.2
  • 88
    • 79951518651 scopus 로고    scopus 로고
    • Modeling allosteric signal propagation using protein structure networks
    • doi:10.1186/1471-2105-12-S1-S23
    • Park K, Kim D (2011) Modeling allosteric signal propagation using protein structure networks. BMC Bioinform 12(Suppl 1):S23. doi:10.1186/1471-2105-12-S1- S23
    • (2011) BMC Bioinform , vol.12 , Issue.SUPPL. 1
    • Park, K.1    Kim, D.2
  • 89
    • 84867666852 scopus 로고    scopus 로고
    • Structure-based rebuilding of coevolutionary information reveals functional modules in rhodopsin structure
    • doi:10.1016/j.bbapap.2012.05.015
    • Park K, Kim D (2012) Structure-based rebuilding of coevolutionary information reveals functional modules in rhodopsin structure. Biochim Biophys Acta. doi:10.1016/j.bbapap.2012.05.015
    • (2012) Biochim Biophys Acta
    • Park, K.1    Kim, D.2
  • 90
    • 84864205788 scopus 로고    scopus 로고
    • xPyder: A PyMOL plugin to analyze coupled residues and their networks in protein structures
    • doi:10.1021/ci300213c
    • Pasi M, Tiberti M, Arrigoni A, Papaleo E (2012) xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures. J Chem Inf Model 52(7):1865-1874. doi:10.1021/ci300213c
    • (2012) J Chem Inf Model , vol.52 , Issue.7 , pp. 1865-1874
    • Pasi, M.1    Tiberti, M.2    Arrigoni, A.3    Papaleo, E.4
  • 91
    • 25944437904 scopus 로고    scopus 로고
    • Dynamical and correlation properties of the internet
    • doi:10.1103/PhysRevLett.87.258701
    • Pastor-Satorras R, Vazquez A, Vespignani A (2001) Dynamical and correlation properties of the internet. Phys Rev Lett 87(25):258701. doi:10.1103/PhysRevLett.87.258701
    • (2001) Phys Rev Lett , vol.87 , Issue.25 , pp. 258701
    • Pastor-Satorras, R.1    Vazquez, A.2    Vespignani, A.3
  • 92
    • 77949382576 scopus 로고    scopus 로고
    • Substrate uptake and protein stability relationship in mammalian histidine decarboxylase
    • doi:10.1002/prot.22587
    • Pino-Angeles A, Morreale A, Negri A, Sanchez-Jimenez F, Moya-Garcia AA (2010) Substrate uptake and protein stability relationship in mammalian histidine decarboxylase. Proteins 78(1):154-161. doi:10.1002/prot.22587
    • (2010) Proteins , vol.78 , Issue.1 , pp. 154-161
    • Pino-Angeles, A.1    Morreale, A.2    Negri, A.3    Sanchez-Jimenez, F.4    Moya-Garcia, A.A.5
  • 93
    • 33748290192 scopus 로고    scopus 로고
    • Classification of Protein-DNA Complexes Based on Structural Descriptors
    • DOI 10.1016/j.str.2006.06.018, PII S0969212606003029
    • Prabakaran P, Siebers JG, Ahmad S, Gromiha MM, Singarayan MG, Sarai A (2006) Classification of protein-DNA complexes based on structural descriptors. Structure 14(9):1355-1367. doi:10.1016/j.str.2006.06.018 (Pubitemid 44331615)
    • (2006) Structure , vol.14 , Issue.9 , pp. 1355-1367
    • Prabakaran, P.1    Siebers, J.G.2    Ahmad, S.3    Gromiha, M.M.4    Singarayan, M.G.5    Sarai, A.6
  • 96
    • 4043129033 scopus 로고    scopus 로고
    • Interaction of DNA with clusters of amino acids in proteins
    • DOI 10.1093/nar/gkh733
    • Sathyapriya R, Vishveshwara S (2004) Interaction of DNA with clusters of amino acids in proteins. Nucleic Acids Res 32(14):4109-4118. doi:10.1093/nar/gkh733 (Pubitemid 39232283)
    • (2004) Nucleic Acids Research , vol.32 , Issue.14 , pp. 4109-4118
    • Sathyapriya, R.1    Vishveshwara, S.2
  • 97
    • 52949123643 scopus 로고    scopus 로고
    • Insights into protein-DNA interactions through structure network analysis
    • doi:10.1371/journal.pcbi.1000170
    • Sathyapriya R, Vijayabaskar MS, Vishveshwara S (2008) Insights into protein-DNA interactions through structure network analysis. PLoS Comput Biol 4(9):e1000170. doi:10.1371/journal.pcbi.1000170
    • (2008) PLoS Comput Biol , vol.4 , Issue.9
    • Sathyapriya, R.1    Vijayabaskar, M.S.2    Vishveshwara, S.3
  • 98
    • 79952498871 scopus 로고    scopus 로고
    • Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces
    • doi:10.1002/jcc.21688
    • Seeber M, Felline A, Raimondi F, Muff S, Friedman R, Rao F, Caflisch A, Fanelli F (2011) Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. J Comput Chem 32(6):1183-1194. doi:10.1002/jcc.21688
    • (2011) J Comput Chem , vol.32 , Issue.6 , pp. 1183-1194
    • Seeber, M.1    Felline, A.2    Raimondi, F.3    Muff, S.4    Friedman, R.5    Rao, F.6    Caflisch, A.7    Fanelli, F.8
  • 99
    • 66149086947 scopus 로고    scopus 로고
    • Dynamical networks in tRNA: Protein complexes
    • doi:10.1073/pnas.0810961106
    • Sethi A, Eargle J, Black AA, Luthey-Schulten Z (2009) Dynamical networks in tRNA: protein complexes. Proc Natl Acad Sci USA 106(16):6620-6625. doi:10.1073/pnas.0810961106
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.16 , pp. 6620-6625
    • Sethi, A.1    Eargle, J.2    Black, A.A.3    Luthey-Schulten, Z.4
  • 100
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software Environment for integrated models of biomolecular interaction networks
    • DOI 10.1101/gr.1239303
    • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498-2504. doi:10.1101/gr.1239303 (Pubitemid 37428274)
    • (2003) Genome Research , vol.13 , Issue.11 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6    Amin, N.7    Schwikowski, B.8    Ideker, T.9
  • 101
    • 0028896311 scopus 로고
    • A relationship between protein stability and protein function
    • doi:10.1073/pnas.92.2.452
    • Shoichet BK, Baase WA, Kuroki R, Matthews BW (1995) A relationship between protein stability and protein function. Proc Natl Acad Sci USA 92(2):452-456. doi:10.1073/pnas.92.2.452
    • (1995) Proc Natl Acad Sci USA , vol.92 , Issue.2 , pp. 452-456
    • Shoichet, B.K.1    Baase, W.A.2    Kuroki, R.3    Matthews, B.W.4
  • 102
    • 17844384545 scopus 로고    scopus 로고
    • Identification of domains and domain interface residues in multidomain proteins from graph spectral method
    • DOI 10.1002/prot.20444
    • Sistla RK, Brinda KV, Vishveshwara S (2005) Identification of domains and domain interface residues in multidomain proteins from graph spectral method. Proteins 59(3):616-626. doi:10.1002/prot.20444 (Pubitemid 40594304)
    • (2005) Proteins: Structure, Function and Genetics , vol.59 , Issue.3 , pp. 616-626
    • Sistla, R.K.1    Brinda, K.V.2    Vishyeshwara, S.3
  • 103
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: New features for data integration and network visualization
    • doi:10.1093/bioinformatics/btq675
    • Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27(3):431-432. doi:10.1093/bioinformatics/btq675
    • (2011) Bioinformatics , vol.27 , Issue.3 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3    Wang, P.L.4    Ideker, T.5
  • 104
    • 4444318641 scopus 로고    scopus 로고
    • Organization, development and function of complex brain networks
    • DOI 10.1016/j.tics.2004.07.008, PII S1364661304001901
    • Sporns O, Chialvo DR, Kaiser M, Hilgetag CC (2004) Organization, development and function of complex brain networks. Trends Cogn Sci 8(9):418-425. doi:10.1016/j.tics.2004.07.008 (Pubitemid 39179905)
    • (2004) Trends in Cognitive Sciences , vol.8 , Issue.9 , pp. 418-425
    • Sporns, O.1    Chialvo, D.R.2    Kaiser, M.3    Hilgetag, C.C.4
  • 105
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • DOI 10.1126/science.1087447
    • Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302(5643):249-255. doi:10.1126/science.1087447 (Pubitemid 37248749)
    • (2003) Science , vol.302 , Issue.5643 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 106
    • 84901446083 scopus 로고    scopus 로고
    • Static and dynamic characteristics of protein contact networks
    • doi:10.1007/s12064-011-0135-y
    • Susan K (2010) Static and dynamic characteristics of protein contact networks. Proteins 40. doi:10.1007/s12064-011-0135-y
    • (2010) Proteins , vol.40
    • Susan, K.1
  • 107
    • 84865247492 scopus 로고    scopus 로고
    • Towards an integrated understanding of the structural characteristics of protein residue networks
    • doi:10.1007/s12064-011-0135-y
    • Susan K (2011) Towards an integrated understanding of the structural characteristics of protein residue networks. Theory Biosci. doi:10.1007/s12064- 011-0135-y
    • (2011) Theory Biosci
    • Susan, K.1
  • 108
    • 84886914488 scopus 로고    scopus 로고
    • Perturbation centrality and turbine: A novel centrality measure obtained using a versatile network dynamics tool
    • doi:10.1371/journal.pone.0078059
    • Szalay KZ, Csermely P (2013) Perturbation centrality and turbine: a novel centrality measure obtained using a versatile network dynamics tool. PLoS ONE 8(10):e78059. doi:10.1371/journal.pone.0078059
    • (2013) PLoS ONE , vol.8 , Issue.10
    • Szalay, K.Z.1    Csermely, P.2
  • 109
    • 77956811912 scopus 로고    scopus 로고
    • Computational inference and analysis of genetic regulatory networks via a supervised combinatorial-optimization pattern
    • doi:10.1186/1752-0509-4-s2-s3
    • Tang B, Wu X, Tan G, Chen SS, Jing Q, Shen B (2010) Computational inference and analysis of genetic regulatory networks via a supervised combinatorial-optimization pattern. BMC Syst Biol 4(Suppl 2):S3. doi:10.1186/1752-0509-4-s2-s3
    • (2010) BMC Syst Biol , vol.4 , Issue.SUPPL. 2
    • Tang, B.1    Wu, X.2    Tan, G.3    Chen, S.S.4    Jing, Q.5    Shen, B.6
  • 110
    • 77955831624 scopus 로고    scopus 로고
    • Analysis and network representation of hotspots in protein interfaces using minimum cut trees
    • doi:10.1002/prot.22741
    • Tuncbag N, Salman FS, Keskin O, Gursoy A (2010) Analysis and network representation of hotspots in protein interfaces using minimum cut trees. Proteins 78(10):2283-2294. doi:10.1002/prot.22741
    • (2010) Proteins , vol.78 , Issue.10 , pp. 2283-2294
    • Tuncbag, N.1    Salman, F.S.2    Keskin, O.3    Gursoy, A.4
  • 111
    • 4644292576 scopus 로고    scopus 로고
    • The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model
    • DOI 10.1038/sj.embor.7400090
    • van Noort V, Snel B, Huynen MA (2004) The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep 5(3):280-284. doi:10.1038/sj.embor.7400090 (Pubitemid 38500108)
    • (2004) EMBO Reports , vol.5 , Issue.3 , pp. 280-284
    • Van Noort, V.1    Snel, B.2    Huynen, M.A.3
  • 112
    • 84865063074 scopus 로고    scopus 로고
    • Exploring residue component contributions to dynamical network models of allostery
    • doi:10.1021/ct300377a
    • Vanwart AT, Eargle J, Luthey-Schulten Z, Amaro RE (2012) Exploring residue component contributions to dynamical network models of allostery. J Chem Theory Comput 8(8):2949-2961. doi:10.1021/ct300377a
    • (2012) J Chem Theory Comput , vol.8 , Issue.8 , pp. 2949-2961
    • Vanwart, A.T.1    Eargle, J.2    Luthey-Schulten, Z.3    Amaro, R.E.4
  • 113
    • 61449181341 scopus 로고    scopus 로고
    • A graph theoretic approach to protein structure selection
    • doi:10.1016/j.artmed.2008.07.016
    • Vassura M, Margara L, Fariselli P, Casadio R (2009) A graph theoretic approach to protein structure selection. Artif Intell Med 45(2-3):229-237. doi:10.1016/j.artmed.2008.07.016
    • (2009) Artif Intell Med , vol.45 , Issue.2-3 , pp. 229-237
    • Vassura, M.1    Margara, L.2    Fariselli, P.3    Casadio, R.4
  • 115
    • 0035252350 scopus 로고    scopus 로고
    • Three key residues form a critical contact network in a protein folding transition state
    • DOI 10.1038/35054591
    • Vendruscolo M, Paci E, Dobson CM, Karplus M (2001) Three key residues form a critical contact network in a protein folding transition state. Nature 409(6820):641-645. doi:10.1038/35054591 (Pubitemid 32154819)
    • (2001) Nature , vol.409 , Issue.6820 , pp. 641-645
    • Vendruscolo, M.1    Paci, E.2    Dobson, C.M.3    Karplus, M.4
  • 116
    • 41349118690 scopus 로고    scopus 로고
    • Smallworld view of the amino acids that play a key role in protein folding
    • doi:10.1103/PhysRevE.65.061910
    • Vendruscolo M, Dokholyan NV, Paci E, Karplus M (2002) Smallworld view of the amino acids that play a key role in protein folding. Phys Rev E Stat Nonlin Soft Matter Phys 65(6 Pt 1):061910. doi:10.1103/PhysRevE.65.061910
    • (2002) Phys Rev E Stat Nonlin Soft Matter Phys , vol.65 , Issue.6 PART 1 , pp. 061910
    • Vendruscolo, M.1    Dokholyan, N.V.2    Paci, E.3    Karplus, M.4
  • 117
    • 78649883885 scopus 로고    scopus 로고
    • Interaction energy based protein structure networks
    • doi:10.1016/j.bpj.2010.08.079
    • Vijayabaskar MS, Vishveshwara S (2010) Interaction energy based protein structure networks. Biophys J 99(11):3704-3715. doi:10.1016/j.bpj.2010.08.079
    • (2010) Biophys J , vol.99 , Issue.11 , pp. 3704-3715
    • Vijayabaskar, M.S.1    Vishveshwara, S.2
  • 118
    • 79955059412 scopus 로고    scopus 로고
    • GraProStr - graphs of protein structures: A tool for constructing the graphs and generating graph parameters for protein structures
    • doi:10.2174/1875036201105010053
    • Vijayabaskar MS, Niranjan V, Vishveshwara S (2011) GraProStr - graphs of protein structures: a tool for constructing the graphs and generating graph parameters for protein structures. Open Bioinform J 5(2011):6. doi:10.2174/1875036201105010053
    • (2011) Open Bioinform J , vol.5 , Issue.2011 , pp. 6
    • Vijayabaskar, M.S.1    Niranjan, V.2    Vishveshwara, S.3
  • 119
    • 65649089458 scopus 로고    scopus 로고
    • Intra and inter-molecular communications through protein structure network
    • doi:10.2174/138920309787847590
    • Vishveshwara S, Ghosh A, Hansia P (2009) Intra and inter-molecular communications through protein structure network. Curr Protein Pept Sci 10(2):146-160. doi:10.2174/138920309787847590
    • (2009) Curr Protein Pept Sci , vol.10 , Issue.2 , pp. 146-160
    • Vishveshwara, S.1    Ghosh, A.2    Hansia, P.3
  • 122
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • DOI 10.1038/30918
    • Watts DJ, Strogatz SH (1998) Collective dynamics of 'small-world' networks. Nature 393(6684):440-442. doi:10.1038/30918 (Pubitemid 28292183)
    • (1998) Nature , vol.393 , Issue.6684 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 123
    • 77956115125 scopus 로고    scopus 로고
    • Effects of time point measurement on the reconstruction of gene regulatory networks
    • (Basel, Switzerland) doi:10.3390/molecules15085354
    • Yan W, Zhu H, Yang Y, Chen J, Zhang Y, Shen B (2010) Effects of time point measurement on the reconstruction of gene regulatory networks. Molecules (Basel, Switzerland) 15(8):5354-5368. doi:10.3390/molecules15085354
    • (2010) Molecules , vol.15 , Issue.8 , pp. 5354-5368
    • Yan, W.1    Zhu, H.2    Yang, Y.3    Chen, J.4    Zhang, Y.5    Shen, B.6
  • 124
    • 58149119413 scopus 로고    scopus 로고
    • Cutoff variation induces different topological properties: A new discovery of amino acid network within protein
    • doi:10.1016/j.jtbi.2008.09.042
    • Yu T, Zou X, Huang SY, Zou XW (2009) Cutoff variation induces different topological properties: a new discovery of amino acid network within protein. J Theor Biol 256(3):408-413. doi:10.1016/j.jtbi.2008.09.042
    • (2009) J Theor Biol , vol.256 , Issue.3 , pp. 408-413
    • Yu, T.1    Zou, X.2    Huang, S.Y.3    Zou, X.W.4
  • 125
    • 84887894373 scopus 로고    scopus 로고
    • Evolution of protein structures and interactions from the perspective of residue contact networks
    • doi:10.1016/j.sbi.2013.07.004
    • Zhang X, Perica T, Teichmann SA (2013) Evolution of protein structures and interactions from the perspective of residue contact networks. Curr Opin Struct Biol 23(6):954-963. doi:10.1016/j.sbi.2013.07.004
    • (2013) Curr Opin Struct Biol , vol.23 , Issue.6 , pp. 954-963
    • Zhang, X.1    Perica, T.2    Teichmann, S.A.3
  • 126
    • 84895515580 scopus 로고    scopus 로고
    • SVR-CAF: An integrated score function for detecting native protein structures among decoys
    • doi:10.1002/prot.24421
    • Zhou J, Yan W, Hu G, Shen B (2013) SVR-CAF: an integrated score function for detecting native protein structures among decoys. Proteins. doi:10.1002/prot.24421
    • (2013) Proteins
    • Zhou, J.1    Yan, W.2    Hu, G.3    Shen, B.4
  • 127
    • 84896357579 scopus 로고    scopus 로고
    • Amino acid network for the discrimination of native protein structures from decoys
    • in press
    • Zhou J, Yan W, Hu G, Shen B (2014) Amino acid network for the discrimination of native protein structures from decoys. Curr Protein Pept Sci 15 (in press)
    • (2014) Curr Protein Pept Sci , vol.15
    • Zhou, J.1    Yan, W.2    Hu, G.3    Shen, B.4


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