-
1
-
-
0035826155
-
Exploring complex networks
-
Strogatz SH. Exploring complex networks. Nature 2001;410:268-276.
-
(2001)
Nature
, vol.410
, pp. 268-276
-
-
Strogatz, S.H.1
-
2
-
-
0242720597
-
Uncovering network systems within protein structures
-
Greene LH, Higman VA. 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
-
3
-
-
0032482432
-
Collective dynamics of "small-world" networks
-
Watts DJ, Strogatz SH. 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
-
4
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabasi AL, Albert R. Emergence of scaling in random networks. Science 1999;286:509-512.
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabasi, A.L.1
Albert, R.2
-
5
-
-
0037012880
-
Specificity and stability in topology of protein networks
-
Maslov S, Sneppen K. Specificity and stability in topology of protein networks. Science 2002;296:910-913.
-
(2002)
Science
, vol.296
, pp. 910-913
-
-
Maslov, S.1
Sneppen, K.2
-
6
-
-
0037199968
-
Hierarchical organization of modularity in metabolic networks
-
Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL. Hierarchical organization of modularity in metabolic networks. Science 2002;297:1551-1555.
-
(2002)
Science
, vol.297
, pp. 1551-1555
-
-
Ravasz, E.1
Somera, A.L.2
Mongru, D.A.3
Oltvai, Z.N.4
Barabasi, A.L.5
-
7
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr SS, Milo R, Mangan S, Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 2002;31:64-68.
-
(2002)
Nat Genet
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
8
-
-
3543099834
-
Evolution and topology in the yeast protein interaction network
-
Wuchty S. Evolution and topology in the yeast protein interaction network. Genome Res 2004;14:1310-1314.
-
(2004)
Genome Res
, vol.14
, pp. 1310-1314
-
-
Wuchty, S.1
-
9
-
-
14644426514
-
Global properties of biological networks
-
Grigorov MG. Global properties of biological networks. Drug Discovery Today 2005;10:365-372.
-
(2005)
Drug Discovery Today
, vol.10
, pp. 365-372
-
-
Grigorov, M.G.1
-
10
-
-
2942544498
-
Protein interaction networks from yeast to human
-
Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM. Protein interaction networks from yeast to human. Curr Opin Struct Biol 2004;14:292-299.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 292-299
-
-
Bork, P.1
Jensen, L.J.2
Von Mering, C.3
Ramani, A.K.4
Lee, I.5
Marcotte, E.M.6
-
11
-
-
0034887573
-
Scale-free behavior in protein domain networks
-
Wuchty S. Scale-free behavior in protein domain networks. Mol Biol Evol 2001;18:1694-1702.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1694-1702
-
-
Wuchty, S.1
-
12
-
-
0035970298
-
Mapping protein family interactions: Intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast
-
Park J, Lappe M, Teichmann SA. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol 2001;307:929-938.
-
(2001)
J Mol Biol
, vol.307
, pp. 929-938
-
-
Park, J.1
Lappe, M.2
Teichmann, S.A.3
-
13
-
-
8544221118
-
Network analysis of protein structures identifies functional residues
-
Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, Venger I, Pietrokovski S. Network analysis of protein structures identifies functional residues. J Mol Biol 2004;344:1135-1146.
-
(2004)
J Mol Biol
, vol.344
, pp. 1135-1146
-
-
Amitai, G.1
Shemesh, A.2
Sitbon, E.3
Shklar, M.4
Netanely, D.5
Venger, I.6
Pietrokovski, S.7
-
14
-
-
4143090730
-
The protein folding network
-
Rao F, Caflisch A. The protein folding network. J Mol Biol 2004;342:299-306.
-
(2004)
J Mol Biol
, vol.342
, pp. 299-306
-
-
Rao, F.1
Caflisch, A.2
-
15
-
-
0035798398
-
Protein family and fold occurrence in genomes: Power-law behaviour and evolutionary model
-
Qian J, Luscombe NM, Gerstein M. Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. J Mol Biol 2001;313:673-681.
-
(2001)
J Mol Biol
, vol.313
, pp. 673-681
-
-
Qian, J.1
Luscombe, N.M.2
Gerstein, M.3
-
17
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 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
-
18
-
-
12844288890
-
The protein structure prediction problem could be solved using the current PDB library
-
Zhang Y, Skolnick J. The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci USA 2005;102:1029-1034.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 1029-1034
-
-
Zhang, Y.1
Skolnick, J.2
-
20
-
-
0034677669
-
Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
-
Wilson CA, Kreychman J, Gerstein, M. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J Mol Biol 2000;297:233-249.
-
(2000)
J Mol Biol
, vol.297
, pp. 233-249
-
-
Wilson, C.A.1
Kreychman, J.2
Gerstein, M.3
-
21
-
-
0036384350
-
One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions
-
Nagano N, Orengo CA, Thornton JM. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol 2002;321:741-765.
-
(2002)
J Mol Biol
, vol.321
, pp. 741-765
-
-
Nagano, N.1
Orengo, C.A.2
Thornton, J.M.3
-
22
-
-
19544389524
-
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
-
Morris RJ, Najmanovich RJ, Kahraman A, Thornton JM. Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics 2005;21:2347-2355.
-
(2005)
Bioinformatics
, vol.21
, pp. 2347-2355
-
-
Morris, R.J.1
Najmanovich, R.J.2
Kahraman, A.3
Thornton, J.M.4
-
23
-
-
0037424601
-
A model for statistical significance of local similarities in structure
-
Stark A, Sunyaev S, Russell RB. A model for statistical significance of local similarities in structure. J Mol Biol 2003;326:1307-1316.
-
(2003)
J Mol Biol
, vol.326
, pp. 1307-1316
-
-
Stark, A.1
Sunyaev, S.2
Russell, R.B.3
-
24
-
-
0041842509
-
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
-
Kinoshita K, Nakamura H. Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci 2003;12:1589-1595.
-
(2003)
Protein Sci
, vol.12
, pp. 1589-1595
-
-
Kinoshita, K.1
Nakamura, H.2
-
25
-
-
0027967593
-
A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures
-
Artymiuk PJ, Poirrette AR, Grindley HM, Rice DW, Willett P. A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J Mol Biol 1994;243:327-344.
-
(1994)
J Mol Biol
, vol.243
, pp. 327-344
-
-
Artymiuk, P.J.1
Poirrette, A.R.2
Grindley, H.M.3
Rice, D.W.4
Willett, P.5
-
27
-
-
0042890523
-
Inferring functional relationships of proteins from local sequence and spatial surface patterns
-
Binkowski TA, Adamian L, Liang J. Inferring functional relationships of proteins from local sequence and spatial surface patterns. J Mol Biol 2003;332:505-526.
-
(2003)
J Mol Biol
, vol.332
, pp. 505-526
-
-
Binkowski, T.A.1
Adamian, L.2
Liang, J.3
-
28
-
-
0036406643
-
A new method to detect related function among proteins independent of sequence and fold homology
-
Schmitt S, Kuhn D, Klebe G. A new method to detect related function among proteins independent of sequence and fold homology. J Mol Biol 2002;323:387-406.
-
(2002)
J Mol Biol
, vol.323
, pp. 387-406
-
-
Schmitt, S.1
Kuhn, D.2
Klebe, G.3
-
29
-
-
0030724039
-
TESS: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites
-
Wallace AC, Borkakoti N, Thornton JM. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci 1997;6:2308-2323.
-
(1997)
Protein Sci
, vol.6
, pp. 2308-2323
-
-
Wallace, A.C.1
Borkakoti, N.2
Thornton, J.M.3
-
30
-
-
2442614144
-
Recognition of functional sites in protein structures
-
Shulman-Peleg A, Nussinov R, Wolfson HJ. Recognition of functional sites in protein structures. J Mol Biol 2004;339:607-633.
-
(2004)
J Mol Biol
, vol.339
, pp. 607-633
-
-
Shulman-Peleg, A.1
Nussinov, R.2
Wolfson, H.J.3
-
31
-
-
0037661398
-
A new bioinformatic approach to detect common 3D sites in protein structures
-
Jambon M, Imberty A, Deleage G, Geourjon C. A new bioinformatic approach to detect common 3D sites in protein structures. Proteins 2003;52:137-145.
-
(2003)
Proteins
, vol.52
, pp. 137-145
-
-
Jambon, M.1
Imberty, A.2
Deleage, G.3
Geourjon, C.4
-
32
-
-
0141506108
-
L/D Protein Ligand Database (PLD): Additional understanding of the nature and specificity of protein-ligand complexes
-
Puvanendrampillai D, Mitchell JB. L/D Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes. Bioinformatics 2003;19:1856-1857.
-
(2003)
Bioinformatics
, vol.19
, pp. 1856-1857
-
-
Puvanendrampillai, D.1
Mitchell, J.B.2
-
33
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998;11:739-747.
-
(1998)
Protein Eng
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
34
-
-
0001338954
-
Simplified amino acid alphabets for protein fold recognition and implications for folding
-
Murphy LR, Wallqvist A, Levy RM. Simplified amino acid alphabets for protein fold recognition and implications for folding. Protein Eng 2000;13:149-152.
-
(2000)
Protein Eng
, vol.13
, pp. 149-152
-
-
Murphy, L.R.1
Wallqvist, A.2
Levy, R.M.3
-
35
-
-
84976668743
-
Algorithm 457: Finding all cliques of an undirected graph
-
Bron C, Kerbosch J. Algorithm 457: Finding all cliques of an undirected graph. Commun ACM 1973;16:575-577.
-
(1973)
Commun ACM
, vol.16
, pp. 575-577
-
-
Bron, C.1
Kerbosch, J.2
-
36
-
-
3543053391
-
Efficient similarity search in protein structure databases by k-clique hashing
-
Weskamp N, Kuhn D, Hullermeier E, Klebe G. Efficient similarity search in protein structure databases by k-clique hashing. Bioinformatics 2004;20:1522-1526.
-
(2004)
Bioinformatics
, vol.20
, pp. 1522-1526
-
-
Weskamp, N.1
Kuhn, D.2
Hullermeier, E.3
Klebe, G.4
-
37
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85:2444-2448.
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
39
-
-
3042616160
-
Biochemistry. De novo design of an enzyme
-
Sterner R, Schmid FX. Biochemistry. De novo design of an enzyme. Science 2004;304:1916-1917.
-
(2004)
Science
, vol.304
, pp. 1916-1917
-
-
Sterner, R.1
Schmid, F.X.2
-
40
-
-
3042655537
-
Computational design of a biologically active enzyme
-
Dwyer MA, Looger LL, Hellinga HW. Computational design of a biologically active enzyme. Science 2004;304:1967-1971.
-
(2004)
Science
, vol.304
, pp. 1967-1971
-
-
Dwyer, M.A.1
Looger, L.L.2
Hellinga, H.W.3
-
41
-
-
4043121114
-
Computational chemogenomics approaches to systematic knowledge-based drug discovery
-
Mestres J. Computational chemogenomics approaches to systematic knowledge-based drug discovery. Curr Opin Drug Discov Dev 2004;7:304-313.
-
(2004)
Curr Opin Drug Discov Dev
, vol.7
, pp. 304-313
-
-
Mestres, J.1
-
42
-
-
41349118690
-
Small-world view of the amino acids that play a key role in protein folding
-
Vendruscolo M, Dokholyan NV, Paci E, Karplus M. Small-world view of the amino acids that play a key role in protein folding. Phys Rev E 2002;65:061910-1-061910-4.
-
(2002)
Phys Rev E
, vol.65
, pp. 619101-619104
-
-
Vendruscolo, M.1
Dokholyan, N.V.2
Paci, E.3
Karplus, M.4
|