-
1
-
-
27144464910
-
Flexible nets: the roles of intrinsic disorder in protein interaction networks
-
10.1111/j.1742-4658.2005.04948.x, 16218947
-
Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN. Flexible nets: the roles of intrinsic disorder in protein interaction networks. FEBS Journal 2005, 272:5129-5148. 10.1111/j.1742-4658.2005.04948.x, 16218947.
-
(2005)
FEBS Journal
, vol.272
, pp. 5129-5148
-
-
Dunker, A.K.1
Cortese, M.S.2
Romero, P.3
Iakoucheva, L.M.4
Uversky, V.N.5
-
2
-
-
0034609791
-
The large-scale organization of metabolic networks
-
10.1038/35036627, 11034217
-
Jeong H, Tombor B, Albert R, Oltvai ZN, BarabaÂsi AL. The large-scale organization of metabolic networks. Nature 2000, 407:651-654. 10.1038/35036627, 11034217.
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltvai, Z.N.4
BarabaÂsi, A.L.5
-
3
-
-
0035799707
-
Lethality and centrality in protein networks
-
10.1038/35075138, 11333967
-
Jeong H, Mason SP, Barabási AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001, 411:41-42. 10.1038/35075138, 11333967.
-
(2001)
Nature
, vol.411
, pp. 41-42
-
-
Jeong, H.1
Mason, S.P.2
Barabási, A.L.3
Oltvai, Z.N.4
-
4
-
-
33645214608
-
Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks
-
Patil A, Nakamura H. Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks. FEBS Letter 2006, 580:2041-2045.
-
(2006)
FEBS Letter
, vol.580
, pp. 2041-2045
-
-
Patil, A.1
Nakamura, H.2
-
5
-
-
37549002450
-
Identification of transient hub proteins and the possible structural basis for their multiple interactions
-
10.1110/ps.073196308, 2144588, 18156468
-
Higurashi M, Ishida T, Kinoshita K. Identification of transient hub proteins and the possible structural basis for their multiple interactions. Protein Sci 2008, 17:72-78. 10.1110/ps.073196308, 2144588, 18156468.
-
(2008)
Protein Sci
, vol.17
, pp. 72-78
-
-
Higurashi, M.1
Ishida, T.2
Kinoshita, K.3
-
6
-
-
29144485503
-
Accounting for global protein deformability during protein-protein and protein-ligand docking
-
May A, Zacharias M. Accounting for global protein deformability during protein-protein and protein-ligand docking. Biochim Biophys Acta 2005, 1754:225-231.
-
(2005)
Biochim Biophys Acta
, vol.1754
, pp. 225-231
-
-
May, A.1
Zacharias, M.2
-
7
-
-
36749057349
-
Implicit flexibility in protein docking: cross-docking and local refinement
-
10.1002/prot.21698, 17671977
-
Król M, Chaleil RAG, Tournier AL, Bates PA. Implicit flexibility in protein docking: cross-docking and local refinement. Proteins 2007, 69:750-757. 10.1002/prot.21698, 17671977.
-
(2007)
Proteins
, vol.69
, pp. 750-757
-
-
Król, M.1
Chaleil, R.A.G.2
Tournier, A.L.3
Bates, P.A.4
-
8
-
-
36749006579
-
Docking and scoring protein complexes: CAPRI 3rd edition
-
10.1002/prot.21804, 17918726
-
Lensink MF, Méndez R, Wodak SJ. Docking and scoring protein complexes: CAPRI 3rd edition. Proteins 2007, 69:704-718. 10.1002/prot.21804, 17918726.
-
(2007)
Proteins
, vol.69
, pp. 704-718
-
-
Lensink, M.F.1
Méndez, R.2
Wodak, S.J.3
-
9
-
-
36749035257
-
Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility
-
10.1002/prot.21735, 17803217
-
May A, Zacharias M. Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility. Proteins 2007, 69:774-780. 10.1002/prot.21735, 17803217.
-
(2007)
Proteins
, vol.69
, pp. 774-780
-
-
May, A.1
Zacharias, M.2
-
10
-
-
38549097715
-
Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
-
10.1002/prot.21579, 17729269
-
May A, Zacharias M. Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking. Proteins 2008, 70:794-809. 10.1002/prot.21579, 17729269.
-
(2008)
Proteins
, vol.70
, pp. 794-809
-
-
May, A.1
Zacharias, M.2
-
11
-
-
15244355250
-
The relationship between the flexibility of proteins and their conformational states on forming protein-porotein complexes with an application to protein-protein docking
-
10.1016/j.jmb.2005.01.058, 15784265
-
Smith GR, Sternberg MJE, Bates PA. The relationship between the flexibility of proteins and their conformational states on forming protein-porotein complexes with an application to protein-protein docking. J Mol Biol 2005, 347:1077-1101. 10.1016/j.jmb.2005.01.058, 15784265.
-
(2005)
J Mol Biol
, vol.347
, pp. 1077-1101
-
-
Smith, G.R.1
Sternberg, M.J.E.2
Bates, P.A.3
-
12
-
-
0038185195
-
Effect of local shape modifications of molecular surfaces on rigid-body protein-protein docking
-
10.1093/proeng/gzg021, 12702797
-
Heifetz A, Eisenstein M. Effect of local shape modifications of molecular surfaces on rigid-body protein-protein docking. Protein Engineering 2003, 16:179-185. 10.1093/proeng/gzg021, 12702797.
-
(2003)
Protein Engineering
, vol.16
, pp. 179-185
-
-
Heifetz, A.1
Eisenstein, M.2
-
13
-
-
21644440105
-
Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI
-
Carter P, Lesk VI, Islam SA, Sternberg MJE. Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI. Proteins 2006, 60:281-288.
-
(2006)
Proteins
, vol.60
, pp. 281-288
-
-
Carter, P.1
Lesk, V.I.2
Islam, S.A.3
Sternberg, M.J.E.4
-
14
-
-
0042622381
-
LGA: a method for finding 3D similarities in protein structures
-
Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acid Research 2003, 31:3370-3374.
-
(2003)
Nucleic Acid Research
, vol.31
, pp. 3370-3374
-
-
Zemla, A.1
-
15
-
-
0346962971
-
Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions
-
10.1021/jm030331x, 14711306
-
Deng Z, Chuaqui C, Singh J. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J Med Chem 2004, 47:337-344. 10.1021/jm030331x, 14711306.
-
(2004)
J Med Chem
, vol.47
, pp. 337-344
-
-
Deng, Z.1
Chuaqui, C.2
Singh, J.3
-
16
-
-
33846933784
-
Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
-
10.1021/ci600342e, 17238265
-
Marcou G, Rognan D. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J Chem Inf Model 2007, 47:195-207. 10.1021/ci600342e, 17238265.
-
(2007)
J Chem Inf Model
, vol.47
, pp. 195-207
-
-
Marcou, G.1
Rognan, D.2
-
17
-
-
22144464877
-
Structure of calmodulin comlexed with an olfactory CNG channel fragment and role of central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family
-
10.1007/s10858-005-0165-1, 15803393
-
Contessa GM, Orsale M, Melino S, Torre V, Paci M, Desideri A, Cicero DO. Structure of calmodulin comlexed with an olfactory CNG channel fragment and role of central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family. J Biomol NMR 2005, 31:185-199. 10.1007/s10858-005-0165-1, 15803393.
-
(2005)
J Biomol NMR
, vol.31
, pp. 185-199
-
-
Contessa, G.M.1
Orsale, M.2
Melino, S.3
Torre, V.4
Paci, M.5
Desideri, A.6
Cicero, D.O.7
-
18
-
-
0032834002
-
A novel target recognition revealed by calmodulin in complex with Ca2+-calmodulin-dependent kinase kinase
-
10.1038/12271, 10467092
-
Osawa M, Tokumitsu H, Swindells MB, Kurihara H, Orita M, Shibanuma T, Furuya T, Ikura M. A novel target recognition revealed by calmodulin in complex with Ca2+-calmodulin-dependent kinase kinase. Nat Struct Biol 1999, 6:819-924. 10.1038/12271, 10467092.
-
(1999)
Nat Struct Biol
, vol.6
, pp. 819-924
-
-
Osawa, M.1
Tokumitsu, H.2
Swindells, M.B.3
Kurihara, H.4
Orita, M.5
Shibanuma, T.6
Furuya, T.7
Ikura, M.8
-
19
-
-
0033592312
-
NMR solution structure of a complex of calmodulin with a binding peptide of the Ca2+ pump
-
10.1021/bi9908235, 10493800
-
Elshorst B, Hennig M, Foeresterling H, Diener A, Maurer M, Schulte P, Schwalbe H, Griesinger C, Jrebs J, Schmid H, Vorherr T, Carafoli E. NMR solution structure of a complex of calmodulin with a binding peptide of the Ca2+ pump. Biochemistry 1999, 38:12320-12332. 10.1021/bi9908235, 10493800.
-
(1999)
Biochemistry
, vol.38
, pp. 12320-12332
-
-
Elshorst, B.1
Hennig, M.2
Foeresterling, H.3
Diener, A.4
Maurer, M.5
Schulte, P.6
Schwalbe, H.7
Griesinger, C.8
Jrebs, J.9
Schmid, H.10
Vorherr, T.11
Carafoli, E.12
-
20
-
-
0029160568
-
Calcium-induced conformational transition revealed by the solution structure of apo calmodulin
-
10.1038/nsb0995-758, 7552747
-
Zhang M, Tanaka T, Ikura M. Calcium-induced conformational transition revealed by the solution structure of apo calmodulin. Nat struct biol 1995, 2:758-767. 10.1038/nsb0995-758, 7552747.
-
(1995)
Nat struct biol
, vol.2
, pp. 758-767
-
-
Zhang, M.1
Tanaka, T.2
Ikura, M.3
-
21
-
-
0038526303
-
ZDOCK: and initial-stage protein-docking algorithm
-
10.1002/prot.10389, 12784371
-
Chen R, Li L, Weng Z. ZDOCK: and initial-stage protein-docking algorithm. Proteins 2003, 52:80-87. 10.1002/prot.10389, 12784371.
-
(2003)
Proteins
, vol.52
, pp. 80-87
-
-
Chen, R.1
Li, L.2
Weng, Z.3
-
22
-
-
0037093643
-
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
-
10.1002/prot.10092, 11948782
-
Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002, 47:281-294. 10.1002/prot.10092, 11948782.
-
(2002)
Proteins
, vol.47
, pp. 281-294
-
-
Chen, R.1
Weng, Z.2
-
23
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
10.1110/ps.03154503, 2323997, 12930999
-
Canutescu AA, Shelenkov AA, Dunbrack RL. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003, 12:2001-2014. 10.1110/ps.03154503, 2323997, 12930999.
-
(2003)
Protein Sci
, vol.12
, pp. 2001-2014
-
-
Canutescu, A.A.1
Shelenkov, A.A.2
Dunbrack, R.L.3
-
24
-
-
34248513078
-
ZRANK: reranking protein docking predictions with an optimized energy function
-
10.1002/prot.21373, 17373710
-
Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 2007, 67:1078-1086. 10.1002/prot.21373, 17373710.
-
(2007)
Proteins
, vol.67
, pp. 1078-1086
-
-
Pierce, B.1
Weng, Z.2
-
25
-
-
0028922586
-
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions
-
10.1093/protein/8.2.127, 7630882
-
Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995, 8:127-134. 10.1093/protein/8.2.127, 7630882.
-
(1995)
Protein Eng
, vol.8
, pp. 127-134
-
-
Wallace, A.C.1
Laskowski, R.A.2
Thornton, J.M.3
-
26
-
-
58149411184
-
Features of similarity
-
Tversky A. Features of similarity. Psychol Rev 1977, 84:327-352.
-
(1977)
Psychol Rev
, vol.84
, pp. 327-352
-
-
Tversky, A.1
-
27
-
-
0037835585
-
Analysis and display of the size dependence of chemical similarity coefficients
-
Holliday JD, Salim N, Whittle M, Willet P. Analysis and display of the size dependence of chemical similarity coefficients. J Chem Inf Comput Sci 2003, 43:819-828.
-
(2003)
J Chem Inf Comput Sci
, vol.43
, pp. 819-828
-
-
Holliday, J.D.1
Salim, N.2
Whittle, M.3
Willet, P.4
|