-
1
-
-
12144290243
-
Structure-based assembly of protein complexes in yeast
-
Aloy P, Bottcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L, Russell RB. Structure-based assembly of protein complexes in yeast. Science 2004; 303: 2026-2029.
-
(2004)
Science
, vol.303
, pp. 2026-2029
-
-
Aloy, P.1
Bottcher, B.2
Ceulemans, H.3
Leutwein, C.4
Mellwig, C.5
Fischer, S.6
Gavin, A.C.7
Bork, P.8
Superti-Furga, G.9
Serrano, L.10
Russell, R.B.11
-
2
-
-
50649096663
-
Analyzing protein interaction networks using structural information
-
Kiel C, Beltrao P, Serrano L. Analyzing protein interaction networks using structural information. Annu Rev Biochem 2008; 77: 415-441.
-
(2008)
Annu Rev Biochem
, vol.77
, pp. 415-441
-
-
Kiel, C.1
Beltrao, P.2
Serrano, L.3
-
3
-
-
79956188706
-
Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces
-
Tuncbag N, Gursoy A, Keskin O. Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces. Phys Biol 2011; 8: 035006.
-
(2011)
Phys Biol
, vol.8
, pp. 035006
-
-
Tuncbag, N.1
Gursoy, A.2
Keskin, O.3
-
5
-
-
33646472024
-
High-resolution protein-protein docking
-
Gray JJ. High-resolution protein-protein docking. Curr Opin Struct Biol 2006; 16: 183-193.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 183-193
-
-
Gray, J.J.1
-
6
-
-
0036606483
-
Principles of docking: an overview of search algorithms and a guide to scoring functions
-
Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002; 47: 409-443.
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
7
-
-
77955391393
-
The HADDOCK web server for data-driven biomolecular docking
-
de Vries SJ, van Dijk M, Bonvin AM. The HADDOCK web server for data-driven biomolecular docking. Nat Protoc 2010; 5: 883-897.
-
(2010)
Nat Protoc
, vol.5
, pp. 883-897
-
-
de Vries, S.J.1
van Dijk, M.2
Bonvin, A.M.3
-
8
-
-
42649122289
-
3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm
-
Lesk VI, Sternberg MJ. 3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm. Bioinformatics 2008; 24: 1137-1144.
-
(2008)
Bioinformatics
, vol.24
, pp. 1137-1144
-
-
Lesk, V.I.1
Sternberg, M.J.2
-
9
-
-
34250882254
-
pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
-
Cheng TM, Blundell TL, Fernandez-Recio J. pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking. Proteins 2007; 68: 503-515.
-
(2007)
Proteins
, vol.68
, pp. 503-515
-
-
Cheng, T.M.1
Blundell, T.L.2
Fernandez-Recio, J.3
-
10
-
-
78149422216
-
Protein-protein docking tested in blind predictions: the CAPRI experiment
-
Janin J. Protein-protein docking tested in blind predictions: the CAPRI experiment. Mol Biosyst 2010; 6: 2351-2362.
-
(2010)
Mol Biosyst
, vol.6
, pp. 2351-2362
-
-
Janin, J.1
-
11
-
-
1842861590
-
Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications
-
Wodak SJ, Mendez R. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 2004; 14: 242-249.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 242-249
-
-
Wodak, S.J.1
Mendez, R.2
-
12
-
-
77952068704
-
Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark
-
Kastritis PL, Bonvin AM. Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark. J Proteome Res 2010; 9: 2216-2225.
-
(2010)
J Proteome Res
, vol.9
, pp. 2216-2225
-
-
Kastritis, P.L.1
Bonvin, A.M.2
-
13
-
-
79952164519
-
On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking
-
Feliu E, Aloy P, Oliva B. On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking. Protein Sci 2011; 20: 529-541.
-
(2011)
Protein Sci
, vol.20
, pp. 529-541
-
-
Feliu, E.1
Aloy, P.2
Oliva, B.3
-
14
-
-
0030602896
-
A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique
-
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J Mol Biol 1996; 260: 604-620.
-
(1996)
J Mol Biol
, vol.260
, pp. 604-620
-
-
Tsai, C.J.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
15
-
-
0029988383
-
Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences
-
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. Crit Rev Biochem Mol Biol 1996; 31: 127-152.
-
(1996)
Crit Rev Biochem Mol Biol
, vol.31
, pp. 127-152
-
-
Tsai, C.J.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
16
-
-
1842405464
-
Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect
-
Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci 1997; 6: 53-64.
-
(1997)
Protein Sci
, vol.6
, pp. 53-64
-
-
Tsai, C.J.1
Lin, S.L.2
Wolfson, H.J.3
Nussinov, R.4
-
17
-
-
0030768266
-
Structural motifs at protein-protein interfaces: protein cores versus two-state and three-state model complexes
-
Tsai CJ, Xu D, Nussinov R. Structural motifs at protein-protein interfaces: protein cores versus two-state and three-state model complexes. Protein Sci 1997; 6: 1793-1805.
-
(1997)
Protein Sci
, vol.6
, pp. 1793-1805
-
-
Tsai, C.J.1
Xu, D.2
Nussinov, R.3
-
18
-
-
0031868211
-
Protein folding via binding and vice versa
-
Tsai CJ, Xu D, Nussinov R. Protein folding via binding and vice versa. Fold Des 1998; 3: R71-R80.
-
(1998)
Fold Des
, vol.3
-
-
Tsai, C.J.1
Xu, D.2
Nussinov, R.3
-
19
-
-
47849091218
-
Architectures and functional coverage of protein-protein interfaces
-
Tuncbag N, Gursoy A, Guney E, Nussinov R, Keskin O. Architectures and functional coverage of protein-protein interfaces. J Mol Biol 2008; 381: 785-802.
-
(2008)
J Mol Biol
, vol.381
, pp. 785-802
-
-
Tuncbag, N.1
Gursoy, A.2
Guney, E.3
Nussinov, R.4
Keskin, O.5
-
20
-
-
22244465254
-
Protein-protein interactions: organization, cooperativity and mapping in a bottom-up systems biology approach
-
Keskin O, Ma B, Rogale K, Gunasekaran K, Nussinov R. Protein-protein interactions: organization, cooperativity and mapping in a bottom-up systems biology approach. Phys Biol 2005; 2: S24-S35.
-
(2005)
Phys Biol
, vol.2
-
-
Keskin, O.1
Ma, B.2
Rogale, K.3
Gunasekaran, K.4
Nussinov, R.5
-
21
-
-
17144366191
-
Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways
-
Keskin O, Nussinov R. Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways. Protein Eng Des Sel 2005; 18: 11-24.
-
(2005)
Protein Eng Des Sel
, vol.18
, pp. 11-24
-
-
Keskin, O.1
Nussinov, R.2
-
22
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy P, Russell RB. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 2002; 99: 5896-5901.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
23
-
-
0041384252
-
In silico identification of functional protein interfaces
-
Bell RE, Ben-Tal N. In silico identification of functional protein interfaces. Comp Funct Genomics 2003; 4: 420-423.
-
(2003)
Comp Funct Genomics
, vol.4
, pp. 420-423
-
-
Bell, R.E.1
Ben-Tal, N.2
-
24
-
-
2542445427
-
ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information
-
Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 2003; 19: 163-164.
-
(2003)
Bioinformatics
, vol.19
, pp. 163-164
-
-
Glaser, F.1
Pupko, T.2
Paz, I.3
Bell, R.E.4
Bechor-Shental, D.5
Martz, E.6
Ben-Tal, N.7
-
25
-
-
11844249426
-
Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues
-
Keskin O, Ma B, Nussinov R. Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol 2005; 345: 1281-1294.
-
(2005)
J Mol Biol
, vol.345
, pp. 1281-1294
-
-
Keskin, O.1
Ma, B.2
Nussinov, R.3
-
26
-
-
1842507022
-
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications
-
Keskin O, Tsai CJ, Wolfson H, Nussinov R. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci 2004; 13: 1043-1055.
-
(2004)
Protein Sci
, vol.13
, pp. 1043-1055
-
-
Keskin, O.1
Tsai, C.J.2
Wolfson, H.3
Nussinov, R.4
-
27
-
-
43149092276
-
Principles of protein-protein interactions: what are the preferred ways for proteins to interact?
-
Keskin O, Gursoy A, Ma B, Nussinov R. Principles of protein-protein interactions: what are the preferred ways for proteins to interact? Chem Rev 2008; 108: 1225-1244.
-
(2008)
Chem Rev
, vol.108
, pp. 1225-1244
-
-
Keskin, O.1
Gursoy, A.2
Ma, B.3
Nussinov, R.4
-
28
-
-
20844454090
-
Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces
-
Aytuna AS, Gursoy A, Keskin O. Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 2005; 21): 2850-2855.
-
(2005)
Bioinformatics
, vol.21
, pp. 2850-2855
-
-
Aytuna, A.S.1
Gursoy, A.2
Keskin, O.3
-
29
-
-
23144463510
-
PRISM: protein interactions by structural matching
-
Ogmen U, Keskin O, Aytuna AS, Nussinov R, Gursoy A. PRISM: protein interactions by structural matching. Nucleic Acids Res 2005; 33: W331-W336.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Ogmen, U.1
Keskin, O.2
Aytuna, A.S.3
Nussinov, R.4
Gursoy, A.5
-
30
-
-
36749058849
-
Docking without docking: ISEARCH-prediction of interactions using known interfaces
-
Gunther S, May P, Hoppe A, Frommel C, Preissner R. Docking without docking: ISEARCH-prediction of interactions using known interfaces. Proteins 2007; 69: 839-844.
-
(2007)
Proteins
, vol.69
, pp. 839-844
-
-
Gunther, S.1
May, P.2
Hoppe, A.3
Frommel, C.4
Preissner, R.5
-
31
-
-
77957959671
-
Docking by structural similarity at protein-protein interfaces
-
Sinha R, Kundrotas PJ, Vakser IA. Docking by structural similarity at protein-protein interfaces. Proteins 2010; 78: 3235-3241.
-
(2010)
Proteins
, vol.78
, pp. 3235-3241
-
-
Sinha, R.1
Kundrotas, P.J.2
Vakser, I.A.3
-
32
-
-
79960387064
-
Dimer interface of the effector domain of nonstructural protein 1 from influenza A virus: an interface with multiple functions
-
Aramini JM, Ma LC, Zhou L, Schauder CM, Hamilton K, Amer BR, Mack TR, Lee HW, Ciccosanti CT, Zhao L, Xiao R, Krug RM, Montelione GT. Dimer interface of the effector domain of nonstructural protein 1 from influenza A virus: an interface with multiple functions. J Biol Chem 2011; 286: 26050-26060.
-
(2011)
J Biol Chem
, vol.286
, pp. 26050-26060
-
-
Aramini, J.M.1
Ma, L.C.2
Zhou, L.3
Schauder, C.M.4
Hamilton, K.5
Amer, B.R.6
Mack, T.R.7
Lee, H.W.8
Ciccosanti, C.T.9
Zhao, L.10
Xiao, R.11
Krug, R.M.12
Montelione, G.T.13
-
33
-
-
85052273120
-
Accuracy of protein-protein binding sites in high-throughput template-based modeling
-
Kundrotas PJ, Vakser IA. Accuracy of protein-protein binding sites in high-throughput template-based modeling. PLoS Comput Biol 2010; 6: e1000727.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Kundrotas, P.J.1
Vakser, I.A.2
-
34
-
-
80052411919
-
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM
-
Tuncbag N, Gursoy A, Nussinov R, Keskin O. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc 2011; 6: 1341-1354.
-
(2011)
Nat Protoc
, vol.6
, pp. 1341-1354
-
-
Tuncbag, N.1
Gursoy, A.2
Nussinov, R.3
Keskin, O.4
-
35
-
-
77951232176
-
FiberDock: flexible induced-fit backbone refinement in molecular docking
-
Mashiach E, Nussinov R, Wolfson HJ. FiberDock: flexible induced-fit backbone refinement in molecular docking. Proteins 2010; 78: 1503-1519.
-
(2010)
Proteins
, vol.78
, pp. 1503-1519
-
-
Mashiach, E.1
Nussinov, R.2
Wolfson, H.J.3
-
36
-
-
0032776303
-
Molecular interaction map of the mammalian cell cyclecontrol and DNA repair systems
-
Kohn KW. Molecular interaction map of the mammalian cell cyclecontrol and DNA repair systems. Mol Biol Cell 1999; 10: 2703-2734.
-
(1999)
Mol Biol Cell
, vol.10
, pp. 2703-2734
-
-
Kohn, K.W.1
-
37
-
-
57349132441
-
Protein-protein docking benchmark version 3.0
-
Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins 2008; 73: 705-709.
-
(2008)
Proteins
, vol.73
, pp. 705-709
-
-
Hwang, H.1
Pierce, B.2
Mintseris, J.3
Janin, J.4
Weng, Z.5
-
38
-
-
77954294794
-
HotPoint: hot spot prediction server for protein interfaces
-
Tuncbag N, Keskin O, Gursoy A. HotPoint: hot spot prediction server for protein interfaces. Nucleic Acids Res 2010; 38 (suppl): W402-W406.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.SUPPL.
-
-
Tuncbag, N.1
Keskin, O.2
Gursoy, A.3
-
39
-
-
0004014257
-
-
University College, London: Department of Biochemistry and Molecular Biology
-
Hubbard SJ, Thornton JM. NACCESS. University College, London: Department of Biochemistry and Molecular Biology; 1993.
-
(1993)
NACCESS
-
-
Hubbard, S.J.1
Thornton, J.M.2
-
40
-
-
0025719208
-
Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques
-
Nussinov R, Wolfson HJ. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc Natl Acad Sci USA 1991; 88: 10495-10499.
-
(1991)
Proc Natl Acad Sci USA
, vol.88
, pp. 10495-10499
-
-
Nussinov, R.1
Wolfson, H.J.2
-
41
-
-
2442456104
-
A method for simultaneous alignment of multiple protein structures
-
Shatsky M, Nussinov R, Wolfson HJ. A method for simultaneous alignment of multiple protein structures. Proteins 2004; 56: 143-156.
-
(2004)
Proteins
, vol.56
, pp. 143-156
-
-
Shatsky, M.1
Nussinov, R.2
Wolfson, H.J.3
-
42
-
-
79961022281
-
The association of heavy and light chain variable domains in antibodies: implications for antigen specificity
-
Chailyan A, Marcatili P, Tramontano A. The association of heavy and light chain variable domains in antibodies: implications for antigen specificity. FEBS J 2011; 278: 2858-2866.
-
(2011)
FEBS J
, vol.278
, pp. 2858-2866
-
-
Chailyan, A.1
Marcatili, P.2
Tramontano, A.3
-
43
-
-
79954608309
-
New benchmark metrics for protein-protein docking methods
-
Gao M, Skolnick J. New benchmark metrics for protein-protein docking methods. Proteins 2011; 79: 1623-1634.
-
(2011)
Proteins
, vol.79
, pp. 1623-1634
-
-
Gao, M.1
Skolnick, J.2
-
45
-
-
0347755535
-
The database of interacting proteins: 2004 update
-
Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The database of interacting proteins: 2004 update. Nucleic Acids Res 2004; 32: D449-D451.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Salwinski, L.1
Miller, C.S.2
Smith, A.J.3
Pettit, F.K.4
Bowie, J.U.5
Eisenberg, D.6
-
46
-
-
33846073818
-
MINT: the Molecular INTeraction database
-
Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G. MINT: the Molecular INTeraction database. Nucleic Acids Res 2007; 35: D572-D574.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Chatr-aryamontri, A.1
Ceol, A.2
Palazzi, L.M.3
Nardelli, G.4
Schneider, M.V.5
Castagnoli, L.6
Cesareni, G.7
-
47
-
-
0037245913
-
BIND: the biomolecular interaction network database
-
Bader GD, Betel D, Hogue CW. BIND: the biomolecular interaction network database. Nucleic Acids Res 2003; 31: 248-250.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 248-250
-
-
Bader, G.D.1
Betel, D.2
Hogue, C.W.3
-
48
-
-
33846047770
-
IntAct-open source resource for molecular interaction data
-
Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H. IntAct-open source resource for molecular interaction data. Nucleic Acids Res 2007; 35: D561-D565.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Kerrien, S.1
Alam-Faruque, Y.2
Aranda, B.3
Bancarz, I.4
Bridge, A.5
Derow, C.6
Dimmer, E.7
Feuermann, M.8
Friedrichsen, A.9
Huntley, R.10
Kohler, C.11
Khadake, J.12
Leroy, C.13
Liban, A.14
Lieftink, C.15
Montecchi-Palazzi, L.16
Orchard, S.17
Risse, J.18
Robbe, K.19
Roechert, B.20
Thorneycroft, D.21
Zhang, Y.22
Apweiler, R.23
Hermjakob, H.24
more..
-
49
-
-
78651324347
-
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
-
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2011; 39: D561-D568.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Szklarczyk, D.1
Franceschini, A.2
Kuhn, M.3
Simonovic, M.4
Roth, A.5
Minguez, P.6
Doerks, T.7
Stark, M.8
Muller, J.9
Bork, P.10
Jensen, L.J.11
von Mering, C.12
|