-
1
-
-
78751613300
-
Link prediction in complex networks: A survey
-
Lü L, Zhou T, (2011) Link prediction in complex networks: A survey. Physica A 390: 1150-1170.
-
(2011)
Physica A
, vol.390
, pp. 1150-1170
-
-
Lü, L.1
Zhou, T.2
-
2
-
-
34249751638
-
The Link-Prediction Problem for Social Networks
-
Liben-Nowell D, Kleinberg J, (2007) The Link-Prediction Problem for Social Networks. J Am Soc Inf Sci Tech 58: 1019-1031.
-
(2007)
J Am Soc Inf Sci Tech
, vol.58
, pp. 1019-1031
-
-
Liben-Nowell, D.1
Kleinberg, J.2
-
3
-
-
84877580262
-
Structure and dynamics of molecular networks: A novel paradigm of drug discovery A comprehensive review
-
Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R, (2013) Structure and dynamics of molecular networks: A novel paradigm of drug discovery A comprehensive review. Pharmacology & Therapeutic In press.
-
(2013)
Pharmacology & Therapeutic In Press
-
-
Csermely, P.1
Korcsmáros, T.2
Kiss, H.J.M.3
London, G.4
Nussinov, R.5
-
4
-
-
84872250417
-
A Structural Perspective on Protein-Protein Interactions in Macromolecular Assemblies
-
In: Zacharias M editor London: Imperial College Press
-
Bahadur RP (2010) A Structural Perspective on Protein-Protein Interactions in Macromolecular Assemblies. In: Zacharias M editor. Protein-Protein Complexes: Analysis, Modeling and Drug Design. London: Imperial College Press. pp. 25-45.
-
(2010)
Protein-Protein Complexes: Analysis, Modeling and Drug Design
, pp. 25-45
-
-
Bahadur, R.P.1
-
5
-
-
34047202181
-
Deciphering protein-protein interactions. Part I. Experimental techniques and databases
-
Shoemaker BA, Panchenko AR, (2007) Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput Biol 3: e42.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Shoemaker, B.A.1
Panchenko, A.R.2
-
6
-
-
24944442468
-
Effect of sampling on topology predictions of protein-protein interaction networks
-
Han JD, Dupuy D, Bertin N, Cusick ME, Vidal M, (2005) Effect of sampling on topology predictions of protein-protein interaction networks. Nat Biotechnol 23: 839-844.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 839-844
-
-
Han, J.D.1
Dupuy, D.2
Bertin, N.3
Cusick, M.E.4
Vidal, M.5
-
7
-
-
38949138554
-
Computational Prediction of Protein-Protein Interactions
-
Skrabanek L, Saini HK, Bader GD, Enright AJ, (2008) Computational Prediction of Protein-Protein Interactions. Mol Biotechnol 38: 1-17.
-
(2008)
Mol Biotechnol
, vol.38
, pp. 1-17
-
-
Skrabanek, L.1
Saini, H.K.2
Bader, G.D.3
Enright, A.J.4
-
8
-
-
34247586171
-
Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners
-
Shoemaker BA, Panchenko AR, (2007) Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol 3: e43.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Shoemaker, B.A.1
Panchenko, A.R.2
-
9
-
-
20844454090
-
Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces
-
Aytuna AS, Gursoy A, Keskin O, (2005) Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces. Bioinformatics 21: 2850-2855.
-
(2005)
Bioinformatics
, vol.21
, pp. 2850-2855
-
-
Aytuna, A.S.1
Gursoy, A.2
Keskin, O.3
-
10
-
-
0036468385
-
Prediction of protein-protein interactions by docking methods
-
Smith GR, Sternberg MJ, (2002) Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 12: 28-35.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 28-35
-
-
Smith, G.R.1
Sternberg, M.J.2
-
11
-
-
68849117733
-
Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression
-
De Bodt S, Proost S, Vandepoele K, Rouzé P, Van de Peer Y, (2009) Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics 10: 288.
-
(2009)
BMC Genomics
, vol.10
, pp. 288
-
-
De Bodt, S.1
Proost, S.2
Vandepoele, K.3
Rouzé, P.4
Van de Peer, Y.5
-
12
-
-
0035023445
-
Predicting protein-protein interactions from primary structure
-
Bock JR, Gough DA, (2001) Predicting protein-protein interactions from primary structure. Bioinformatics 17: 455-460.
-
(2001)
Bioinformatics
, vol.17
, pp. 455-460
-
-
Bock, J.R.1
Gough, D.A.2
-
13
-
-
28944450149
-
Prediction of protein-protein interactions using random decision forest framework
-
Chen XW, Liu M, (2005) Prediction of protein-protein interactions using random decision forest framework. Bioinformatics 21: 4394-4400.
-
(2005)
Bioinformatics
, vol.21
, pp. 4394-4400
-
-
Chen, X.W.1
Liu, M.2
-
14
-
-
77952305592
-
Large-scale prediction of protein-protein interactions from structures
-
Hue M, Riffle M, Vert JP, Noble WS, (2010) Large-scale prediction of protein-protein interactions from structures. BMC Bioinformatics 11: 144.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 144
-
-
Hue, M.1
Riffle, M.2
Vert, J.P.3
Noble, W.S.4
-
15
-
-
67649494468
-
Protein-protein interaction based on pairwise similarity
-
Zaki N, Lazarova-Molnar S, El-Hajj W, Campbell P, (2009) Protein-protein interaction based on pairwise similarity. BMC Bioinformatics 10: 150.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 150
-
-
Zaki, N.1
Lazarova-Molnar, S.2
El-Hajj, W.3
Campbell, P.4
-
16
-
-
84859839007
-
Can simple codon pair usage predict protein-protein interaction?
-
Zhou Y, Zhou YS, He F, Song J, Zhang Z, (2012) Can simple codon pair usage predict protein-protein interaction?. Mol Biosyst 8: 1396-1404.
-
(2012)
Mol Biosyst
, vol.8
, pp. 1396-1404
-
-
Zhou, Y.1
Zhou, Y.S.2
He, F.3
Song, J.4
Zhang, Z.5
-
17
-
-
0142052944
-
A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data
-
Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, et al. (2003) A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data. Science 302: 449-453.
-
(2003)
Science
, vol.302
, pp. 449-453
-
-
Jansen, R.1
Yu, H.2
Greenbaum, D.3
Kluger, Y.4
Krogan, N.J.5
-
18
-
-
2942541277
-
Predicting co-complexed protein pairs using genomic and proteomic data integration
-
Zhang LV, Wong SL, King OD, Roth FP, (2004) Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 5: 38.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 38
-
-
Zhang, L.V.1
Wong, S.L.2
King, O.D.3
Roth, F.P.4
-
19
-
-
24744435534
-
Kernel methods for predicting protein-protein interactions
-
Ben-Hur A, Noble WS, (2005) Kernel methods for predicting protein-protein interactions. Bioinformatics 21: i38-i46.
-
(2005)
Bioinformatics
, vol.21
-
-
Ben-Hur, A.1
Noble, W.S.2
-
20
-
-
23444452564
-
Probabilistic model of the human protein-protein interaction network
-
Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, et al. (2005) Probabilistic model of the human protein-protein interaction network. Nat Biotechnol 23: 951-959.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 951-959
-
-
Rhodes, D.R.1
Tomlins, S.A.2
Varambally, S.3
Mahavisno, V.4
Barrette, T.5
-
21
-
-
61449249266
-
Sequence-based prediction of protein interaction sites with an integrative method
-
Chen XW, Jeong JC, (2009) Sequence-based prediction of protein interaction sites with an integrative method. Bioinformatics 25: 585-591.
-
(2009)
Bioinformatics
, vol.25
, pp. 585-591
-
-
Chen, X.W.1
Jeong, J.C.2
-
22
-
-
48349138497
-
Computational Methods For Predicting Protein-Protein Interactions
-
Pitre S, Alamgir M, Green JR, Dumontier M, Dehne F, et al. (2008) Computational Methods For Predicting Protein-Protein Interactions. Adv Biochem Eng Biotechnol 110: 247-267.
-
(2008)
Adv Biochem Eng Biotechnol
, vol.110
, pp. 247-267
-
-
Pitre, S.1
Alamgir, M.2
Green, J.R.3
Dumontier, M.4
Dehne, F.5
-
23
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB, (1973) Principles that govern the folding of protein chains. Science 181: 223-230.
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
-
24
-
-
34248371273
-
Predicting protein-protein interactions based only on sequences information
-
Shen J, Zhang J, Luo X, Zhu W, Yu K, et al. (2007) Predicting protein-protein interactions based only on sequences information. Proc Natl Acad Sci USA 104: 4337-4341.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 4337-4341
-
-
Shen, J.1
Zhang, J.2
Luo, X.3
Zhu, W.4
Yu, K.5
-
25
-
-
44349159560
-
Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
-
Guo Y, Yu L, Wen Z, Li M, (2008) Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences. Nucleic Acids Res 36: 3025-3030.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 3025-3030
-
-
Guo, Y.1
Yu, L.2
Wen, Z.3
Li, M.4
-
26
-
-
77953488986
-
PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment
-
Guo Y, Li M, Pu X, Li G, Guang X, et al. (2010) PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment. BMC Res Notes 3: 145.
-
(2010)
BMC Res Notes
, vol.3
, pp. 145
-
-
Guo, Y.1
Li, M.2
Pu, X.3
Li, G.4
Guang, X.5
-
27
-
-
84856267563
-
SPPS: a sequence-based method for predicting probability of protein-protein interaction partners
-
Liu X, Liu B, Huang Z, Shi T, Chen Y, et al. (2012) SPPS: a sequence-based method for predicting probability of protein-protein interaction partners. PloS One 7: e30938.
-
(2012)
PloS One
, vol.7
-
-
Liu, X.1
Liu, B.2
Huang, Z.3
Shi, T.4
Chen, Y.5
-
28
-
-
16344384583
-
Effect of training datasets on support vector machine prediction of protein-protein interactions
-
Lo SL, Cai CZ, Chen YZ, Chung MC, (2005) Effect of training datasets on support vector machine prediction of protein-protein interactions. Proteomics 5: 876-884.
-
(2005)
Proteomics
, vol.5
, pp. 876-884
-
-
Lo, S.L.1
Cai, C.Z.2
Chen, Y.Z.3
Chung, M.C.4
-
29
-
-
13444262436
-
Predicting protein-protein interactions using signature products
-
Martin S, Roe D, Faulon JL, (2005) Predicting protein-protein interactions using signature products. Bioinformatics 21: 218-226.
-
(2005)
Bioinformatics
, vol.21
, pp. 218-226
-
-
Martin, S.1
Roe, D.2
Faulon, J.L.3
-
30
-
-
33646871614
-
An ensemble of K-local hyperplanes for predicting protein-protein interactions
-
Nanni L, Lumini A, (2006) An ensemble of K-local hyperplanes for predicting protein-protein interactions. Bioinformatics 22: 1207-1210.
-
(2006)
Bioinformatics
, vol.22
, pp. 1207-1210
-
-
Nanni, L.1
Lumini, A.2
-
31
-
-
80054804148
-
Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation
-
Ren X, Wang YC, Wang Y, Zhang XS, Deng NY, (2011) Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation. BMC Bioinformatics 12: 409.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 409
-
-
Ren, X.1
Wang, Y.C.2
Wang, Y.3
Zhang, X.S.4
Deng, N.Y.5
-
32
-
-
19544369864
-
An evolution based classifier for prediction of protein interfaces without using protein structures
-
Res I, Mihalek I, Lichtarge O, (2005) An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics 21: 2496-2501.
-
(2005)
Bioinformatics
, vol.21
, pp. 2496-2501
-
-
Res, I.1
Mihalek, I.2
Lichtarge, O.3
-
33
-
-
70949106297
-
Exploiting amino acid composition for predicting protein-protein interactions
-
Roy S, Martinez D, Platero H, Lane T, Werner-Washburne M, (2009) Exploiting amino acid composition for predicting protein-protein interactions. PloS One 4: e7813.
-
(2009)
PloS One
, vol.4
-
-
Roy, S.1
Martinez, D.2
Platero, H.3
Lane, T.4
Werner-Washburne, M.5
-
34
-
-
77951667947
-
Predicting protein-protein interactions from sequence using correlation coefficient and high-quality interaction dataset
-
Shi MG, Xia JF, Li XL, Huang DS, (2010) Predicting protein-protein interactions from sequence using correlation coefficient and high-quality interaction dataset. Amino Acids 38: 891-899.
-
(2010)
Amino Acids
, vol.38
, pp. 891-899
-
-
Shi, M.G.1
Xia, J.F.2
Li, X.L.3
Huang, D.S.4
-
35
-
-
77950545785
-
Predicting protein-protein interactions in unbalanced data using the primary structure of proteins
-
Yu CY, Chou LC, Chang DT, (2010) Predicting protein-protein interactions in unbalanced data using the primary structure of proteins. BMC Bioinformatics 11: 167.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 167
-
-
Yu, C.Y.1
Chou, L.C.2
Chang, D.T.3
-
36
-
-
77957821742
-
Simple sequence-based kernels do not predict protein-protein interactions
-
Yu J, Guo M, Needham CJ, Huang Y, Cai L, et al. (2010) Simple sequence-based kernels do not predict protein-protein interactions. Bioinformatics 26: 2610-2614.
-
(2010)
Bioinformatics
, vol.26
, pp. 2610-2614
-
-
Yu, J.1
Guo, M.2
Needham, C.J.3
Huang, Y.4
Cai, L.5
-
38
-
-
34248532098
-
Comprehensive Statistical Analysis of Residues Interaction Specificity at Protein-Protein Interfaces
-
Anashkina A, Kuznetsov E, Esipova N, Tumanyan V, (2007) Comprehensive Statistical Analysis of Residues Interaction Specificity at Protein-Protein Interfaces. Proteins 67: 1060-1077.
-
(2007)
Proteins
, vol.67
, pp. 1060-1077
-
-
Anashkina, A.1
Kuznetsov, E.2
Esipova, N.3
Tumanyan, V.4
-
39
-
-
0030028728
-
Principles of protein-protein interactions
-
Jones S, Thornton JM, (1996) Principles of protein-protein interactions. Proc Natl Acad Sci USA 93: 13-20.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 13-20
-
-
Jones, S.1
Thornton, J.M.2
-
40
-
-
0037388679
-
Protein-protein interactions as a target for drugs in proteomics
-
Archakov AI, Govorun VM, Dubanov AV, Ivanov ID, Veselovsky AV, et al. (2003) Protein-protein interactions as a target for drugs in proteomics. Proteomics 3: 380-391.
-
(2003)
Proteomics
, vol.3
, pp. 380-391
-
-
Archakov, A.I.1
Govorun, V.M.2
Dubanov, A.V.3
Ivanov, I.D.4
Veselovsky, A.V.5
-
41
-
-
0025275610
-
On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands
-
Padlan EA, (1990) On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands. Proteins 7: 112-124.
-
(1990)
Proteins
, vol.7
, pp. 112-124
-
-
Padlan, E.A.1
-
42
-
-
0025964038
-
Structure, function and properties of antibody binding sites
-
Mian IS, Bradwell AR, Olson AJ, (1991) Structure, function and properties of antibody binding sites. J Mol Biol 217: 133-151.
-
(1991)
J Mol Biol
, vol.217
, pp. 133-151
-
-
Mian, I.S.1
Bradwell, A.R.2
Olson, A.J.3
-
43
-
-
0036300780
-
Solution Structures of UBA Domains Reveal a Conserved Hydrophobic Surface for Protein-Protein Interactions
-
Mueller TD, Feigon J, (2002) Solution Structures of UBA Domains Reveal a Conserved Hydrophobic Surface for Protein-Protein Interactions. J Mol Biol 319: 1243-1255.
-
(2002)
J Mol Biol
, vol.319
, pp. 1243-1255
-
-
Mueller, T.D.1
Feigon, J.2
-
44
-
-
0037229456
-
Analysing Six Types of Protein-Protein Interfaces
-
Ofran Y, Rost B, (2003) Analysing Six Types of Protein-Protein Interfaces. J Mol Biol 325: 377-387.
-
(2003)
J Mol Biol
, vol.325
, pp. 377-387
-
-
Ofran, Y.1
Rost, B.2
-
45
-
-
16644386648
-
The importance of disulfide bridging
-
Swaisgood HE, (2005) The importance of disulfide bridging. Biotechnol Adv 23: 71-73.
-
(2005)
Biotechnol Adv
, vol.23
, pp. 71-73
-
-
Swaisgood, H.E.1
-
46
-
-
80054923089
-
Revisiting the negative example sampling problem for predicting protein-protein interactions
-
Park Y, Marcotte EM, (2011) Revisiting the negative example sampling problem for predicting protein-protein interactions. Bioinformatics 27: 3024-3028.
-
(2011)
Bioinformatics
, vol.27
, pp. 3024-3028
-
-
Park, Y.1
Marcotte, E.M.2
-
47
-
-
78651328883
-
The Biogrid Interaction Database: 2011 update
-
Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, et al. (2011) The Biogrid Interaction Database: 2011 update. Nucleic Acids Res 39: D698-D704.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Stark, C.1
Breitkreutz, B.J.2
Chatr-Aryamontri, A.3
Boucher, L.4
Oughtred, R.5
-
48
-
-
75549083088
-
The Negatome Database: a reference set of non-interacting protein pairs
-
Smialowski P, Pagel P, Wong P, Brauner B, Dunger I, et al. (2010) The Negatome Database: a reference set of non-interacting protein pairs. Nucleic Acids Res 38: D540-D544.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Smialowski, P.1
Pagel, P.2
Wong, P.3
Brauner, B.4
Dunger, I.5
-
49
-
-
78651319979
-
Ongoing and future developments at the Universal Protein Resource
-
UniProt Consortium
-
UniProt Consortium (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 39: D214-D219.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
-
50
-
-
33747816816
-
PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
-
Li ZR, Lin HH, Han LY, Jiang L, Chen X, et al. (2006) PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res 34: W32-W37.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Li, Z.R.1
Lin, H.H.2
Han, L.Y.3
Jiang, L.4
Chen, X.5
-
53
-
-
0030211964
-
Bagging predictors
-
Breiman L, (1996) Bagging predictors. Machine Learning 24: 123-140.
-
(1996)
Machine Learning
, vol.24
, pp. 123-140
-
-
Breiman, L.1
-
55
-
-
78651011426
-
Probability tables for individual comparisons by ranking methods
-
Wilcoxon F, (1947) Probability tables for individual comparisons by ranking methods. Biometrics 3: 119-122.
-
(1947)
Biometrics
, vol.3
, pp. 119-122
-
-
Wilcoxon, F.1
|