-
1
-
-
33745684683
-
Weighted and unweighted network of amino acids within protein
-
Aftabuddin M., Kundu S. Weighted and unweighted network of amino acids within protein. Phys. A: Stat. Mech. Appl. 2006, 369:895-904.
-
(2006)
Phys. A: Stat. Mech. Appl.
, vol.369
, pp. 895-904
-
-
Aftabuddin, M.1
Kundu, S.2
-
2
-
-
0034633749
-
Classes of small-world networks
-
Amaral L.A., Scala A., Barthelemy M., Stanley H.E. Classes of small-world networks. Proc. Natl. Acad. Sci. USA 2000, 97:11149-11152.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 11149-11152
-
-
Amaral, L.A.1
Scala, A.2
Barthelemy, M.3
Stanley, H.E.4
-
3
-
-
34547909602
-
Assortative mixing in protein contact networks and protein folding kinetics
-
Bagler G., Sinha S. Assortative mixing in protein contact networks and protein folding kinetics. Bioinformatics 2007, 23:1760-1767.
-
(2007)
Bioinformatics
, vol.23
, pp. 1760-1767
-
-
Bagler, G.1
Sinha, S.2
-
4
-
-
38049119840
-
The effect of backbone on the small-world properties of protein contact maps
-
Bartoli L., Fariselli P., Casadio R. The effect of backbone on the small-world properties of protein contact maps. Phys. Biol. 2007, 4:L1-L5.
-
(2007)
Phys. Biol.
, vol.4
-
-
Bartoli, L.1
Fariselli, P.2
Casadio, R.3
-
5
-
-
0033954256
-
The protein data bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acids Res. 2000, 28:235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
6
-
-
33748143748
-
Structural determinants of the rate of protein evolution in yeast
-
Bloom J.D., Drummond D.A., Arnold F.H., Wilke C.O. Structural determinants of the rate of protein evolution in yeast. Mol. Biol. Evol. 2006, 23:1751-1761.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 1751-1761
-
-
Bloom, J.D.1
Drummond, D.A.2
Arnold, F.H.3
Wilke, C.O.4
-
7
-
-
0033969946
-
Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica
-
Bustamante C.D., Townsend J.P., Hartl D.L. Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Mol. Biol. Evol. 2000, 17:301-308.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 301-308
-
-
Bustamante, C.D.1
Townsend, J.P.2
Hartl, D.L.3
-
8
-
-
43349094507
-
The igraph software package for complex network research
-
Csardi G., Nepusz T. The igraph software package for complex network research. Int. J.: Complex Syst. 2006, 1695:1695.
-
(2006)
Int. J.: Complex Syst.
, vol.1695
, pp. 1695
-
-
Csardi, G.1
Nepusz, T.2
-
9
-
-
12944331889
-
Small-world network approach to identify key residues in protein-protein interaction
-
del Sol A., O'Meara P. Small-world network approach to identify key residues in protein-protein interaction. Proteins 2005, 58:672-682.
-
(2005)
Proteins
, vol.58
, pp. 672-682
-
-
del Sol, A.1
O'Meara, P.2
-
10
-
-
84875170915
-
Protein contact networks: an emerging paradigm in chemistry
-
Di Paola L., De Ruvo M., Paci P., Santoni D., Giuliani A. Protein contact networks: an emerging paradigm in chemistry. Chem. Rev. 2012, 113:1598-1613.
-
(2012)
Chem. Rev.
, vol.113
, pp. 1598-1613
-
-
Di Paola, L.1
De Ruvo, M.2
Paci, P.3
Santoni, D.4
Giuliani, A.5
-
11
-
-
0041673352
-
Structural determinant of protein designability
-
England J.L., Shakhnovich E.I. Structural determinant of protein designability. Phys. Rev. Lett. 2003, 90:218101.
-
(2003)
Phys. Rev. Lett.
, vol.90
, pp. 218101
-
-
England, J.L.1
Shakhnovich, E.I.2
-
12
-
-
0037177560
-
Evolutionary rate in the protein interaction network
-
Fraser H.B., Hirsh A.E., Steinmetz L.M., Scharfe C., Feldman M.W. Evolutionary rate in the protein interaction network. Science 2002, 296:750-752.
-
(2002)
Science
, vol.296
, pp. 750-752
-
-
Fraser, H.B.1
Hirsh, A.E.2
Steinmetz, L.M.3
Scharfe, C.4
Feldman, M.W.5
-
13
-
-
84865730611
-
A set of measures of centrality based on betweenness
-
Freeman L. A set of measures of centrality based on betweenness. Sociometry 1977, 40:35-41.
-
(1977)
Sociometry
, vol.40
, pp. 35-41
-
-
Freeman, L.1
-
14
-
-
84898995964
-
Network properties of protein structures
-
Ganesh B., Sinha S. Network properties of protein structures. Physica A 2004, 346:5.
-
(2004)
Physica A
, vol.346
, pp. 5
-
-
Ganesh, B.1
Sinha, S.2
-
15
-
-
72449143779
-
Proteins as networks: a mesoscopic approach using haemoglobin molecule as case study
-
Giuliani A., Di Paola L., Setola R. Proteins as networks: a mesoscopic approach using haemoglobin molecule as case study. Curr. Proteomics 2009, 6:235-245.
-
(2009)
Curr. Proteomics
, vol.6
, pp. 235-245
-
-
Giuliani, A.1
Di Paola, L.2
Setola, R.3
-
16
-
-
0020972782
-
Theoretical studies of protein folding
-
Go N. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 1983, 12:183-210.
-
(1983)
Annu. Rev. Biophys. Bioeng.
, vol.12
, pp. 183-210
-
-
Go, N.1
-
17
-
-
40849108375
-
Vulnerability and hierarchy of complex networks.
-
Gol[U+05F3]dshtein, V., Koganov, G.A., Surdutovich, G.I., 2004. Vulnerability and hierarchy of complex networks. http://www.elsevier.com/xml/linking-roles/preprint.
-
(2004)
-
-
Gol'dshtein, V.1
Koganov, G.A.2
Surdutovich, G.I.3
-
18
-
-
0242720597
-
Uncovering network systems within protein structures
-
Greene L.H., Higman V.A. Uncovering network systems within protein structures. J. Mol. Biol. 2003, 334:781-791.
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 781-791
-
-
Greene, L.H.1
Higman, V.A.2
-
19
-
-
84896335283
-
Residue interaction network analysis of Dronpa and a DNA clamp
-
Hu G., Yan W., Zhou J., Shen B. Residue interaction network analysis of Dronpa and a DNA clamp. J. Theor. Biol. 2014, 348:55-64.
-
(2014)
J. Theor. Biol.
, vol.348
, pp. 55-64
-
-
Hu, G.1
Yan, W.2
Zhou, J.3
Shen, B.4
-
20
-
-
84878604130
-
The topology and dynamics of protein complexes: insights from intra-molecular network theory
-
Hu G., Zhou J., Yan W., Chen J., Shen B. The topology and dynamics of protein complexes: insights from intra-molecular network theory. Curr. Protein Pept. Sci. 2013, 14:121-132.
-
(2013)
Curr. Protein Pept. Sci.
, vol.14
, pp. 121-132
-
-
Hu, G.1
Zhou, J.2
Yan, W.3
Chen, J.4
Shen, B.5
-
21
-
-
33847686233
-
Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula
-
Ingvarsson P.K. Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula. Mol. Biol. Evol. 2007, 24:836-844.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 836-844
-
-
Ingvarsson, P.K.1
-
22
-
-
34248185088
-
Construction and application of the weighted amino acid network based on energy
-
Jiao X., Chang S., Li C.H., Chen W.Z., Wang C.X. Construction and application of the weighted amino acid network based on energy. Phys. Rev. E: Stat. Nonlinear Soft Matter Phys. 2007, 75:051903.
-
(2007)
Phys. Rev. E: Stat. Nonlinear Soft Matter Phys.
, vol.75
, pp. 051903
-
-
Jiao, X.1
Chang, S.2
Li, C.H.3
Chen, W.Z.4
Wang, C.X.5
-
23
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
24
-
-
41949141017
-
Proteins as networks: usefulness of graph theory in protein science
-
Krishnan A., Zbilut J.P., Tomita M., Giuliani A. Proteins as networks: usefulness of graph theory in protein science. Curr. Protein Pept. Sci. 2008, 9:28-38.
-
(2008)
Curr. Protein Pept. Sci.
, vol.9
, pp. 28-38
-
-
Krishnan, A.1
Zbilut, J.P.2
Tomita, M.3
Giuliani, A.4
-
25
-
-
0002226671
-
Use of the singular value decomposition in regression analysis
-
Mandel J. Use of the singular value decomposition in regression analysis. Am. Stat. 1982, 36:15-24.
-
(1982)
Am. Stat.
, vol.36
, pp. 15-24
-
-
Mandel, J.1
-
26
-
-
16344388218
-
Protein structural influences in rhodopsin evolution
-
Marsh L., Griffiths C.S. Protein structural influences in rhodopsin evolution. Mol. Biol. Evol. 2005, 22:894-904.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 894-904
-
-
Marsh, L.1
Griffiths, C.S.2
-
27
-
-
33846829987
-
The pls package: principal component and partial least squares regression in R
-
Mevik B.r.-H., Wehrens R. The pls package: principal component and partial least squares regression in R. J. Stat. Softw. 2007, 18:1-24.
-
(2007)
J. Stat. Softw.
, vol.18
, pp. 1-24
-
-
Mevik, B.-H.1
Wehrens, R.2
-
28
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
-
Miyazawa S., Jernigan R. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985, 18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.2
-
29
-
-
84861312435
-
Level of gene expression is a major determinant of protein evolution in the viral order mononegavirales
-
Pagan I., Holmes E., Simon-Loriere E. Level of gene expression is a major determinant of protein evolution in the viral order mononegavirales. J. Virol. 2012, 86:5253-5263.
-
(2012)
J. Virol.
, vol.86
, pp. 5253-5263
-
-
Pagan, I.1
Holmes, E.2
Simon-Loriere, E.3
-
30
-
-
33646182934
-
An integrated view of protein evolution
-
Pal C., Papp B., Lercher M.J. An integrated view of protein evolution. Nat. Rev. Genet. 2006, 7:337-348.
-
(2006)
Nat. Rev. Genet.
, vol.7
, pp. 337-348
-
-
Pal, C.1
Papp, B.2
Lercher, M.J.3
-
31
-
-
77956971129
-
A Language and Environment for Statistical Computing.
-
R Development Core Team, 2012. R:
-
R Development Core Team, 2012. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
-
R Foundation for Statistical Computing, Vienna, Austria.
-
-
-
32
-
-
65349169643
-
The correlation of evolutionary rate with pathway position in plant terpenoid biosynthesis
-
Ramsay H., Rieseberg L.H., Ritland K. The correlation of evolutionary rate with pathway position in plant terpenoid biosynthesis. Mol. Biol. Evol. 2009, 26:1045-1053.
-
(2009)
Mol. Biol. Evol.
, vol.26
, pp. 1045-1053
-
-
Ramsay, H.1
Rieseberg, L.H.2
Ritland, K.3
-
33
-
-
80055069190
-
Protein structural modularity and robustness are associated with evolvability
-
Rorick M.M., Wagner G.P. Protein structural modularity and robustness are associated with evolvability. Genome Biol. Evol. 2011, 3:456-475.
-
(2011)
Genome Biol. Evol.
, vol.3
, pp. 456-475
-
-
Rorick, M.M.1
Wagner, G.P.2
-
34
-
-
80052964856
-
Understanding the contribution of synonymous mutations to human disease
-
Sauna Z.E., Kimchi-Sarfaty C. Understanding the contribution of synonymous mutations to human disease. Nat. Rev. Genet. 2011, 12:683-691.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 683-691
-
-
Sauna, Z.E.1
Kimchi-Sarfaty, C.2
-
35
-
-
0242391985
-
RankViaContact: ranking and visualization of amino acid contacts
-
Shen B., Vihinen M. RankViaContact: ranking and visualization of amino acid contacts. Bioinformatics 2003, 19:2161-2162.
-
(2003)
Bioinformatics
, vol.19
, pp. 2161-2162
-
-
Shen, B.1
Vihinen, M.2
-
36
-
-
84901446083
-
Dynamic Characteristics of Protein Contact Networks.
-
Static and [cs.CE]
-
Susan, K., 2010. Static and Dynamic Characteristics of Protein Contact Networks. arXiv:1011.2222 [cs.CE]; http://dx.doi.org/10.1007/s12064-011-0135-y.
-
(2010)
-
-
Susan, K.1
-
37
-
-
84865247492
-
Towards an integrated understanding of the structural characteristics of protein residue networks
-
Susan K. Towards an integrated understanding of the structural characteristics of protein residue networks. Theory Biosci. 2011, 131:61-75.
-
(2011)
Theory Biosci.
, vol.131
, pp. 61-75
-
-
Susan, K.1
-
38
-
-
37349040074
-
On the characterization of energy networks of proteins
-
Veloso C.J., Silveira C.H., Melo R.C., Ribeiro C., Lopes J.C., Santoro M.M., Meira W. On the characterization of energy networks of proteins. Genet. Mol. Res. 2007, 6:799-820.
-
(2007)
Genet. Mol. Res.
, vol.6
, pp. 799-820
-
-
Veloso, C.J.1
Silveira, C.H.2
Melo, R.C.3
Ribeiro, C.4
Lopes, J.C.5
Santoro, M.M.6
Meira, W.7
-
39
-
-
41349118690
-
Small-world view of the amino acids that play a key role in protein folding
-
Vendruscolo M., Dokholyan N.V., Paci E., Karplus M. Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E: Stat. Nonlinear Soft Matter Phys. 2002, 65:061910.
-
(2002)
Phys. Rev. E: Stat. Nonlinear Soft Matter Phys.
, vol.65
, pp. 061910
-
-
Vendruscolo, M.1
Dokholyan, N.V.2
Paci, E.3
Karplus, M.4
-
40
-
-
78649883885
-
Interaction energy based protein structure networks
-
Vijayabaskar M.S., Vishveshwara S. Interaction energy based protein structure networks. Biophys. J. 2010, 99:3704-3715.
-
(2010)
Biophys. J.
, vol.99
, pp. 3704-3715
-
-
Vijayabaskar, M.S.1
Vishveshwara, S.2
-
41
-
-
17244367886
-
Functional genomic analysis of the rates of protein evolution
-
Wall D.P., Hirsh A.E., Fraser H.B., Kumm J., Giaever G., Eisen M.B., Feldman M.W. Functional genomic analysis of the rates of protein evolution. Proc. Natl. Acad. Sci. USA 2005, 102:5483-5488.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 5483-5488
-
-
Wall, D.P.1
Hirsh, A.E.2
Fraser, H.B.3
Kumm, J.4
Giaever, G.5
Eisen, M.B.6
Feldman, M.W.7
-
44
-
-
0032482432
-
Collective dynamics of 'small-world' networks
-
Watts D.J., Strogatz S.H. Collective dynamics of 'small-world' networks. Nature 1998, 393:440-442.
-
(1998)
Nature
, vol.393
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
45
-
-
84901451274
-
The Construction of an Amino acid Network for Understanding Protein Structure and Function.
-
Amino Acids 46, (PMID: 23831698)
-
Yan, W., Zhou, J., Sun, M., Chen, J., Hu, G., Shen, B., 2014. The Construction of an Amino acid Network for Understanding Protein Structure and Function. Amino Acids 46, (PMID: 23831698); http://dx.doi.org/10.1007/s00726-014-1710-6.
-
(2014)
-
-
Yan, W.1
Zhou, J.2
Sun, M.3
Chen, J.4
Hu, G.5
Shen, B.6
-
46
-
-
84878362869
-
Structure-based prediction of the effects of a missense variant on protein stability
-
Yang Y., Chen B., Tan G., Vihinen M., Shen B. Structure-based prediction of the effects of a missense variant on protein stability. Amino Acids 2013, 44:847-855.
-
(2013)
Amino Acids
, vol.44
, pp. 847-855
-
-
Yang, Y.1
Chen, B.2
Tan, G.3
Vihinen, M.4
Shen, B.5
-
47
-
-
0034646196
-
Environment-dependent residue contact energies for proteins
-
Zhang C., Kim S.H. Environment-dependent residue contact energies for proteins. Proc. Natl. Acad. Sci. USA 2000, 97:2550-2555.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 2550-2555
-
-
Zhang, C.1
Kim, S.H.2
-
48
-
-
84895515580
-
SVR_CAF: An integrated score function for detecting native protein structures among decoys
-
Zhou J., Yan W., Hu G., Shen B. SVR_CAF: An integrated score function for detecting native protein structures among decoys. Proteins 2014, 82:556-564.
-
(2014)
Proteins
, vol.82
, pp. 556-564
-
-
Zhou, J.1
Yan, W.2
Hu, G.3
Shen, B.4
-
49
-
-
84896357579
-
Amino acid network for the discrimination of native protein structures from decoys
-
(accepted)
-
Zhou J., Yan W., Hu G., Shen B. Amino acid network for the discrimination of native protein structures from decoys. Curr. Protein Pept. Sci. 2014, 15. (accepted).
-
(2014)
Curr. Protein Pept. Sci.
, vol.15
-
-
Zhou, J.1
Yan, W.2
Hu, G.3
Shen, B.4
-
50
-
-
43149112799
-
Contact density affects protein evolutionary rate from bacteria to animals
-
Zhou T., Drummond D.A., Wilke C.O. Contact density affects protein evolutionary rate from bacteria to animals. J. Mol. Evol. 2008, 66:395-404.
-
(2008)
J. Mol. Evol.
, vol.66
, pp. 395-404
-
-
Zhou, T.1
Drummond, D.A.2
Wilke, C.O.3
|