-
1
-
-
1942456697
-
Recent advances in the development and application of implicit solvent models in biomolecule simulations
-
Feig M., and Brooks III C.L. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 14 2 (2004) 217-224
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, Issue.2
, pp. 217-224
-
-
Feig, M.1
Brooks III, C.L.2
-
2
-
-
0347753603
-
Reduced models of proteins and their applications
-
Kolinski A., and Skolnick J. Reduced models of proteins and their applications. Polymer 45 2 (2004) 511-524
-
(2004)
Polymer
, vol.45
, Issue.2
, pp. 511-524
-
-
Kolinski, A.1
Skolnick, J.2
-
3
-
-
0036013593
-
Statistical mechanics of complex networks
-
Albert R., and Barabási A.-L. Statistical mechanics of complex networks. Rev. Mod. Phys. 74 1 (2002) 47-97
-
(2002)
Rev. Mod. Phys.
, vol.74
, Issue.1
, pp. 47-97
-
-
Albert, R.1
Barabási, A.-L.2
-
5
-
-
0038718854
-
The structure and function of complex networks
-
Newman M.E.J. The structure and function of complex networks. SIAM Rev. 45 2 (2003) 167-256
-
(2003)
SIAM Rev.
, vol.45
, Issue.2
, pp. 167-256
-
-
Newman, M.E.J.1
-
6
-
-
0032482432
-
Collective dynamics of 'small-world' networks
-
Watts D.J., and Strogatz S.H. Collective dynamics of 'small-world' networks. Nature 393 6684 (1998) 440-442
-
(1998)
Nature
, vol.393
, Issue.6684
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
7
-
-
0034633749
-
Classes of small-world networks
-
Amaral L.A.N., Scala A., Barthélémy M., and Stanley H.E. Classes of small-world networks. Proc. Natl. Acad. Sci. USA 97 21 (2000) 11149-11152
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, Issue.21
, pp. 11149-11152
-
-
Amaral, L.A.N.1
Scala, A.2
Barthélémy, M.3
Stanley, H.E.4
-
8
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabási A.-L., and Albert R. Emergence of scaling in random networks. Science 286 5439 (1999) 509-512
-
(1999)
Science
, vol.286
, Issue.5439
, pp. 509-512
-
-
Barabási, A.-L.1
Albert, R.2
-
9
-
-
4243287545
-
Small worlds: how and why
-
Mathias N., and Gopal V. Small worlds: how and why. Phys. Rev. E 63 2 (2001) 021117
-
(2001)
Phys. Rev. E
, vol.63
, Issue.2
, pp. 021117
-
-
Mathias, N.1
Gopal, V.2
-
11
-
-
3042656794
-
Network structures from selection principles
-
Colizza V., Banavar J.R., Maritan A., and Rinaldo A. Network structures from selection principles. Phys. Rev. Lett. 92 19 (2004) 198701
-
(2004)
Phys. Rev. Lett.
, vol.92
, Issue.19
, pp. 198701
-
-
Colizza, V.1
Banavar, J.R.2
Maritan, A.3
Rinaldo, A.4
-
12
-
-
41349118690
-
Small-world view of the amino acids that play a key role in protein folding
-
Vendruscolo M., Dokholyan N.V., Paci E., and Karplus M. Small-world view of the amino acids that play a key role in protein folding. Phys. Rev. E 65 6 (2002) 061910
-
(2002)
Phys. Rev. E
, vol.65
, Issue.6
, pp. 061910
-
-
Vendruscolo, M.1
Dokholyan, N.V.2
Paci, E.3
Karplus, M.4
-
13
-
-
0242720597
-
Uncovering network systems within protein structures
-
Greene L.H., and Higman V.A. Uncovering network systems within protein structures. J. Mol. Biol. 334 4 (2003) 781-791
-
(2003)
J. Mol. Biol.
, vol.334
, Issue.4
, pp. 781-791
-
-
Greene, L.H.1
Higman, V.A.2
-
14
-
-
0346057951
-
Small-world communication of residues and significance for protein dynamics
-
Atilgan A.R., Akan P., and Baysal C. Small-world communication of residues and significance for protein dynamics. Biophys. J. 86 1 (2004) 85-91
-
(2004)
Biophys. J.
, vol.86
, Issue.1
, pp. 85-91
-
-
Atilgan, A.R.1
Akan, P.2
Baysal, C.3
-
15
-
-
9944223645
-
Network properties of protein structures
-
Bagler G., and Sinha S. Network properties of protein structures. Physica A 346 1-2 (2005) 27-33
-
(2005)
Physica A
, vol.346
, Issue.1-2
, pp. 27-33
-
-
Bagler, G.1
Sinha, S.2
-
16
-
-
9944232975
-
Amino acid network within protein
-
Kundu S. Amino acid network within protein. Physica A 346 1-2 (2005) 104-109
-
(2005)
Physica A
, vol.346
, Issue.1-2
, pp. 104-109
-
-
Kundu, S.1
-
17
-
-
0037173002
-
Topological determinants of protein folding
-
Dokholyan N.V., Li L., Ding F., and Shakhnovich E.I. Topological determinants of protein folding. Proc. Natl. Acad. Sci. USA 99 13 (2002) 8637-8641
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, Issue.13
, pp. 8637-8641
-
-
Dokholyan, N.V.1
Li, L.2
Ding, F.3
Shakhnovich, E.I.4
-
18
-
-
0025370815
-
Dominant forces in protein folding
-
Dill K.A. Dominant forces in protein folding. Biochemistry 29 31 (1990) 7133-7155
-
(1990)
Biochemistry
, vol.29
, Issue.31
, pp. 7133-7155
-
-
Dill, K.A.1
-
20
-
-
33751397282
-
-
These data are available under request.
-
-
-
-
21
-
-
0028961335
-
SCOP-a structural classification of proteins database for the investigation of sequences and structures
-
Murzin A., Brenner S., Hubbard T., and Chothia C. SCOP-a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 4 (1995) 536-540
-
(1995)
J. Mol. Biol.
, vol.247
, Issue.4
, pp. 536-540
-
-
Murzin, A.1
Brenner, S.2
Hubbard, T.3
Chothia, C.4
-
22
-
-
0038752085
-
Mixing patterns in networks
-
Newman M.E.J. Mixing patterns in networks. Phys. Rev. E 67 2 (2003) 026126
-
(2003)
Phys. Rev. E
, vol.67
, Issue.2
, pp. 026126
-
-
Newman, M.E.J.1
-
23
-
-
2942566660
-
Cut-offs and finite size effects in scale-free networks
-
Boguñá M., Pastor-Satorras R., and Vespignani A. Cut-offs and finite size effects in scale-free networks. Eur. Phys. J. B 38 2 (2004) 205-209
-
(2004)
Eur. Phys. J. B
, vol.38
, Issue.2
, pp. 205-209
-
-
Boguñá, M.1
Pastor-Satorras, R.2
Vespignani, A.3
-
24
-
-
0031008576
-
Hydrophobicity regained
-
Karplus P.A. Hydrophobicity regained. Protein Sci. 6 (1997) 1302-1307
-
(1997)
Protein Sci.
, vol.6
, pp. 1302-1307
-
-
Karplus, P.A.1
-
25
-
-
0041418222
-
Spatial profiling of protein hydrophobicity: native vs. decoy structures
-
Zhou R., Silverman B.D., Royyuru A.K., and Athma P. Spatial profiling of protein hydrophobicity: native vs. decoy structures. Proteins 52 4 (2003) 561-572
-
(2003)
Proteins
, vol.52
, Issue.4
, pp. 561-572
-
-
Zhou, R.1
Silverman, B.D.2
Royyuru, A.K.3
Athma, P.4
-
26
-
-
24144464469
-
A simple hydrophobicity-based score for profiling protein structures
-
Alves N.A., Aleksenko V., and Hansmann U.H.E. A simple hydrophobicity-based score for profiling protein structures. J. Phys. Condens. Matter 17 18 (2005) S1595-S1606
-
(2005)
J. Phys. Condens. Matter
, vol.17
, Issue.18
-
-
Alves, N.A.1
Aleksenko, V.2
Hansmann, U.H.E.3
-
27
-
-
0035255017
-
Quantitative comparison of the ability of hydropathy scales to recognize surface β-strands in proteins
-
Palliser C.C., and Parry D.A.D. Quantitative comparison of the ability of hydropathy scales to recognize surface β-strands in proteins. Proteins 42 2 (2001) 243-255
-
(2001)
Proteins
, vol.42
, Issue.2
, pp. 243-255
-
-
Palliser, C.C.1
Parry, D.A.D.2
-
28
-
-
0036893044
-
Stability scale and atomic solvation parameters extracted from 1023 mutation experiments
-
Zhou H., and Zhou Y. Stability scale and atomic solvation parameters extracted from 1023 mutation experiments. Proteins 49 (2002) 483-492
-
(2002)
Proteins
, vol.49
, pp. 483-492
-
-
Zhou, H.1
Zhou, Y.2
-
29
-
-
0345827721
-
Quantifying the effect of burial of amino acid residues on protein stability
-
Zhou H., and Zhou Y. Quantifying the effect of burial of amino acid residues on protein stability. Proteins 54 (2004) 315-322
-
(2004)
Proteins
, vol.54
, pp. 315-322
-
-
Zhou, H.1
Zhou, Y.2
-
30
-
-
18744389789
-
Assortative mixing in networks
-
Newman M.E.J. Assortative mixing in networks. Phys. Rev. Lett. 89 20 (2002) 208701
-
(2002)
Phys. Rev. Lett.
, vol.89
, Issue.20
, pp. 208701
-
-
Newman, M.E.J.1
-
32
-
-
0242663620
-
Class of correlated random networks with hidden variables
-
Boguñá M., and Pastor-Satorras R. Class of correlated random networks with hidden variables. Phys. Rev. E 68 3 (2003) 036112
-
(2003)
Phys. Rev. E
, vol.68
, Issue.3
, pp. 036112
-
-
Boguñá, M.1
Pastor-Satorras, R.2
-
33
-
-
0038542266
-
Topology and correlations in structured scale-free networks
-
Vázquez A., Boguñá M., Moreno Y., Pastor-Satorras R., and Vespignani A. Topology and correlations in structured scale-free networks. Phys. Rev. E 67 4 (2003) 046111
-
(2003)
Phys. Rev. E
, vol.67
, Issue.4
, pp. 046111
-
-
Vázquez, A.1
Boguñá, M.2
Moreno, Y.3
Pastor-Satorras, R.4
Vespignani, A.5
-
34
-
-
2942532800
-
Social network growth with assortative mixing
-
Catanzaro M., Caldarelli G., and Pietronero L. Social network growth with assortative mixing. Physica A 338 (2004) 119-124
-
(2004)
Physica A
, vol.338
, pp. 119-124
-
-
Catanzaro, M.1
Caldarelli, G.2
Pietronero, L.3
-
35
-
-
0035639140
-
Birds of feather: homophily in social networks
-
McPherson M., Smith-Lovin L., and Cook J. Birds of feather: homophily in social networks. Ann. Rev. Soc. 27 (2001) 415-444
-
(2001)
Ann. Rev. Soc.
, vol.27
, pp. 415-444
-
-
McPherson, M.1
Smith-Lovin, L.2
Cook, J.3
-
36
-
-
0028856785
-
Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications
-
Fersht A.R. Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc. Natl. Acad. Sci. USA. 92 24 (1995) 10869-10873
-
(1995)
Proc. Natl. Acad. Sci. USA.
, vol.92
, Issue.24
, pp. 10869-10873
-
-
Fersht, A.R.1
-
37
-
-
33751434196
-
-
M. Brede, S. Sinha, Assortative mixing by degree makes a network more unstable, cond-mat/0507710 (2005).
-
-
-
-
38
-
-
0036139093
-
Why are proteins marginally stable
-
Taverna D.M., and Goldstein R.A. Why are proteins marginally stable. Proteins 46 (2002) 105-109
-
(2002)
Proteins
, vol.46
, pp. 105-109
-
-
Taverna, D.M.1
Goldstein, R.A.2
-
39
-
-
0742289618
-
Relation between protein stability, evolution and structure, as probed by carboxylic acid mutations
-
Godoy-Ruiz R., Perez-Jimenez R., Ibara-Molero B., and Sanchez-Ruiz J.M. Relation between protein stability, evolution and structure, as probed by carboxylic acid mutations. J. Mol. Biol. 336 (2004) 313-318
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 313-318
-
-
Godoy-Ruiz, R.1
Perez-Jimenez, R.2
Ibara-Molero, B.3
Sanchez-Ruiz, J.M.4
-
40
-
-
0034310033
-
Models of the small world
-
Newman M.E.J. Models of the small world. J. Stat. Phys. 101 3-4 (2000) 819-841
-
(2000)
J. Stat. Phys.
, vol.101
, Issue.3-4
, pp. 819-841
-
-
Newman, M.E.J.1
|