-
1
-
-
55849109221
-
Quantitative assessment of the structural bias in protein-protein interaction assays
-
Bjorklund,A.K., Light,S., Hedin,L. and Elofsson,A. (2008) Quantitative assessment of the structural bias in protein-protein interaction assays. Proteomics, 8, 4657-4667.
-
(2008)
Proteomics
, vol.8
, pp. 4657-4667
-
-
Bjorklund, A.K.1
Light, S.2
Hedin, L.3
Elofsson, A.4
-
2
-
-
58149218155
-
Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network
-
Simonis,N., Rual,J.F., Carvunis,A.R., Tasan,M., Lemmens,I., Hirozane-Kishikawa,T., Hao,T., Sahalie,J.M., Venkatesan,K., Gebreab,F. et al. (2009) Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nature Methods, 6, 47-54.
-
(2009)
Nature Methods
, vol.6
, pp. 47-54
-
-
Simonis, N.1
Rual, J.F.2
Carvunis, A.R.3
Tasan, M.4
Lemmens, I.5
Hirozane-Kishikawa, T.6
Hao, T.7
Sahalie, J.M.8
Venkatesan, K.9
Gebreab, F.10
-
3
-
-
58149305794
-
An empirical framework for binary interactome mapping
-
Venkatesan,K., Rual,J.F., Vazquez,A., Stelzl,U., Lemmens,I., Hirozane-Kishikawa,T., Hao,T., Zenkner,M., Xin,X., Goh,K.I. et al. (2009) An empirical framework for binary interactome mapping. Nat. Methods, 6, 83-90.
-
(2009)
Nat. Methods
, vol.6
, pp. 83-90
-
-
Venkatesan, K.1
Rual, J.F.2
Vazquez, A.3
Stelzl, U.4
Lemmens, I.5
Hirozane-Kishikawa, T.6
Hao, T.7
Zenkner, M.8
Xin, X.9
Goh, K.I.10
-
4
-
-
3042569597
-
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs
-
Yu,H., Luscombe,N.M., Lu,H.X., Zhu,X., Xia,Y., Han,J.D., Bertin,N., Chung,S., Vidal,M. and Gerstein,M. (2004) Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res., 14, 1107-1118.
-
(2004)
Genome Res
, vol.14
, pp. 1107-1118
-
-
Yu, H.1
Luscombe, N.M.2
Lu, H.X.3
Zhu, X.4
Xia, Y.5
Han, J.D.6
Bertin, N.7
Chung, S.8
Vidal, M.9
Gerstein, M.10
-
5
-
-
30844443758
-
Herpesviral protein networks and their interaction with the human proteome
-
Uetz,P., Dong,Y.A., Zeretzke,C., Atzler,C., Baiker,A., Berger,B., Rajagopala,S.V., Roupelieva,M., Rose,D., Fossum,E. et al. (2006) Herpesviral protein networks and their interaction with the human proteome. Science, 311, 239-242.
-
(2006)
Science
, vol.311
, pp. 239-242
-
-
Uetz, P.1
Dong, Y.A.2
Zeretzke, C.3
Atzler, C.4
Baiker, A.5
Berger, B.6
Rajagopala, S.V.7
Roupelieva, M.8
Rose, D.9
Fossum, E.10
-
6
-
-
33645732240
-
Modeling cellular machinery through biological network comparison
-
Sharan,R. and Ideker,T. (2006) Modeling cellular machinery through biological network comparison. Nat. Biotechnol., 24, 427-433.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 427-433
-
-
Sharan, R.1
Ideker, T.2
-
7
-
-
51349087811
-
Global alignment of multiple protein interaction networks with application to functional orthology detection
-
Singh,R., Xu,J. and Berger,B. (2008) Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc. Natl Acad. Sci. USA, 105, 12763-12768.
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 12763-12768
-
-
Singh, R.1
Xu, J.2
Berger, B.3
-
8
-
-
33646018046
-
Evaluation of different biological data and computational classification methods for use in protein interaction prediction
-
Qi,Y., Bar-Joseph,Z. and Klein-Seetharaman,J. (2006) Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins, 63, 490-500.
-
(2006)
Proteins
, vol.63
, pp. 490-500
-
-
Qi, Y.1
Bar-Joseph, Z.2
Klein-Seetharaman, J.3
-
9
-
-
33745805365
-
Integrated protein interaction networks for 11 microbes
-
Srinivasan,B., Novak,A., Flannick,J., Batzoglou,S. and McAdams,H. (2006) Integrated protein interaction networks for 11 microbes. LNCS, 3909, 1-14.
-
(2006)
LNCS
, vol.3909
, pp. 1-14
-
-
Srinivasan, B.1
Novak, A.2
Flannick, J.3
Batzoglou, S.4
McAdams, H.5
-
10
-
-
58149193234
-
STRING 8-a global view on proteins and their functional interactions in 630 organisms
-
Jensen,L.J., Kuhn,M., Stark,M., Chaffron,S., Creevey,C., Muller,J., Doerks,T., Julien,P., Roth,A., Simonovic,M. et al. (2009) STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res., 37, D412-D416.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Jensen, L.J.1
Kuhn, M.2
Stark, M.3
Chaffron, S.4
Creevey, C.5
Muller, J.6
Doerks, T.7
Julien, P.8
Roth, A.9
Simonovic, M.10
-
11
-
-
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. et al. (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Res., 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
-
12
-
-
33846102842
-
DOMINO: a database of domain-peptide interactions
-
Ceol,A., Chatr-aryamontri,A., Santonico,E., Sacco,R., Castagnoli,L. and Cesareni,G. (2007) DOMINO: a database of domain-peptide interactions. Nucleic Acids Res., 35, D557-D560.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Ceol, A.1
Chatr-aryamontri, A.2
Santonico, E.3
Sacco, R.4
Castagnoli, L.5
Cesareni, G.6
-
13
-
-
0037250151
-
InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes
-
Ng,S.K., Zhang,Z., Tan,S.H. and Lin,K. (2003) InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Res., 31, 251-254.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 251-254
-
-
Ng, S.K.1
Zhang, Z.2
Tan, S.H.3
Lin, K.4
-
14
-
-
34548855730
-
Unequal evolutionary conservation of human protein interactions in interologous networks
-
Brown,K.R. and Jurisica,I. (2007) Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol., 8, R95.
-
(2007)
Genome Biol
, vol.8
-
-
Brown, K.R.1
Jurisica, I.2
-
15
-
-
0033954256
-
The protein data bank
-
Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The protein data bank. Nucleic Acids Res., 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
-
16
-
-
0037197902
-
Interrogating protein interaction networks through structural biology
-
Aloy,P. and Russell,R.B. (2002) Interrogating protein interaction networks through structural biology. Proc. Natl Acad. Sci. USA, 99, 5896-5901.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 5896-5901
-
-
Aloy, P.1
Russell, R.B.2
-
17
-
-
0037340493
-
Development of unified statistical potentials describing protein-protein interactions
-
Lu,H., Lu,L. and Skolnick,J. (2003) Development of unified statistical potentials describing protein-protein interactions. Biophys. J., 84, 1895-1901.
-
(2003)
Biophys. J.
, vol.84
, pp. 1895-1901
-
-
Lu, H.1
Lu, L.2
Skolnick, J.3
-
18
-
-
0038817799
-
Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome
-
Lu,L., Arakaki,A.K., Lu,H. and Skolnick,J. (2003) Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. Genome Res., 13, 1146-1154.
-
(2003)
Genome Res
, vol.13
, pp. 1146-1154
-
-
Lu, L.1
Arakaki, A.K.2
Lu, H.3
Skolnick, J.4
-
19
-
-
39049191929
-
Struct2net: integrating structure into protein-protein interaction prediction
-
Singh,R., Xu,J. and Berger,B. (2006) Struct2net: integrating structure into protein-protein interaction prediction. Pac. Symp. Biocomput., 11, 403-414.
-
(2006)
Pac. Symp. Biocomput.
, vol.11
, pp. 403-414
-
-
Singh, R.1
Xu, J.2
Berger, B.3
-
20
-
-
0037250158
-
InterPreTS: protein interaction prediction through tertiary structure
-
Aloy,P. and Russell,R.B. (2003) InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics, 19, 161-162.
-
(2003)
Bioinformatics
, vol.19
, pp. 161-162
-
-
Aloy, P.1
Russell, R.B.2
-
21
-
-
48449090519
-
HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures
-
Fukuhara,N. and Kawabata,T. (2008) HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures. Nucleic Acids Res., 36, W185-W189.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Fukuhara, N.1
Kawabata, T.2
-
22
-
-
34447286876
-
Prediction of interacting proteins from homology-modeled complex structures using sequence and structure scores
-
Fukuhara,N., Go,N. and Kawabata,T. (2006) Prediction of interacting proteins from homology-modeled complex structures using sequence and structure scores. Biophysics, 3, 13.
-
(2006)
Biophysics
, vol.3
, pp. 13
-
-
Fukuhara, N.1
Go, N.2
Kawabata, T.3
-
23
-
-
58149187896
-
MODBASE, a database of annotated comparative protein structure models and associated resources
-
Pieper,U., Eswar,N., Webb,B.M., Eramian,D., Kelly,L., Barkan,D.T., Carter,H., Mankoo,P., Karchin,R., Marti-Renom,M.A. et al. (2009) MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res., 37, D347-D354.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Pieper, U.1
Eswar, N.2
Webb, B.M.3
Eramian, D.4
Kelly, L.5
Barkan, D.T.6
Carter, H.7
Mankoo, P.8
Karchin, R.9
Marti-Renom, M.A.10
-
24
-
-
69849100180
-
ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs
-
Encinar,J.A., Fernandez-Ballester,G., Sanchez,I.E., Hurtado-Gomez,E., Stricher,F., Beltrao,P. and Serrano,L. (2009) ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs. Bioinformatics, 25, 2418-2424.
-
(2009)
Bioinformatics
, vol.25
, pp. 2418-2424
-
-
Encinar, J.A.1
Fernandez-Ballester, G.2
Sanchez, I.E.3
Hurtado-Gomez, E.4
Stricher, F.5
Beltrao, P.6
Serrano, L.7
-
25
-
-
33745327144
-
An integrated approach to the prediction of domain-domain interactions
-
Lee,H., Deng,M., Sun,F. and Chen,T. (2006) An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics, 7, 269.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 269
-
-
Lee, H.1
Deng, M.2
Sun, F.3
Chen, T.4
-
26
-
-
41849115573
-
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale
-
Wang,H., Segal,E., Ben-Hur,A., Li,Q.R., Vidal,M. and Koller,D. (2007) InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. Genome Biol., 8, R192.
-
(2007)
Genome Biol
, vol.8
-
-
Wang, H.1
Segal, E.2
Ben-Hur, A.3
Li, Q.R.4
Vidal, M.5
Koller, D.6
-
27
-
-
33747853260
-
Structural domain-domain interactions: assessment and comparison with protein-protein interaction data to improve the interactome
-
Prieto,C., De., Las. and Rivas,J. (2006) Structural domain-domain interactions: assessment and comparison with protein-protein interaction data to improve the interactome. Nucleic Acids Res., 34, W298-W302.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Prieto, C.1
De, Las.2
Rivas, J.3
-
28
-
-
13444257903
-
3did: interacting protein domains of known three-dimensional structure
-
Stein,A., Russell,R. and Aloy,P. (2005) 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res., 33, D413-D417.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Stein, A.1
Russell, R.2
Aloy, P.3
-
29
-
-
33846052595
-
SNAPPI-DB: a database and API of structures, iNterfaces and alignments for protein-protein interactions
-
Jefferson,E., Walsh,T., Roberts,T. and Barton,G. (2007) SNAPPI-DB: a database and API of structures, iNterfaces and alignments for protein-protein interactions. Nucleic Acids Res., 35, D580-D589.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Jefferson, E.1
Walsh, T.2
Roberts, T.3
Barton, G.4
-
30
-
-
13844264506
-
iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
-
Finn,R., Marshall,M. and Bateman,A. (2005) iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics, 21, 410-412.
-
(2005)
Bioinformatics
, vol.21
, pp. 410-412
-
-
Finn, R.1
Marshall, M.2
Bateman, A.3
-
31
-
-
18744382508
-
PIBASE: a comprehensive database of structurally defined protein interfaces
-
Davis,F. and Sali,A. (2005) PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics, 21, 1901-1907.
-
(2005)
Bioinformatics
, vol.21
, pp. 1901-1907
-
-
Davis, F.1
Sali, A.2
-
32
-
-
21144432882
-
PSIBASE: a database of Protein Structural Interactome map (PSIMAP)
-
Gong,S., Yoon,G., Jang,I., Bolser,D., Dafas,P., Schroeder,M., Choi,H., Cho,Y., Han,K., Lee,S. et al. (2005) PSIBASE: a database of Protein Structural Interactome map (PSIMAP). Bioinformatics, 21, 2541-2543.
-
(2005)
Bioinformatics
, vol.21
, pp. 2541-2543
-
-
Gong, S.1
Yoon, G.2
Jang, I.3
Bolser, D.4
Dafas, P.5
Schroeder, M.6
Choi, H.7
Cho, Y.8
Han, K.9
Lee, S.10
-
33
-
-
0242330716
-
Assessment of RAPTOR's linear programming approach in CAFASP3
-
Xu,J. and Li,M. (2003) Assessment of RAPTOR's linear programming approach in CAFASP3. Proteins, 53(Suppl. 6), 579-584.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 579-584
-
-
Xu, J.1
Li, M.2
-
34
-
-
74249111445
-
Template-based and free modeling by RAPTOR++ in CASP8
-
Xu,J., Peng,J. and Zhao,F. (2009) Template-based and free modeling by RAPTOR++ in CASP8. Proteins, 77(Suppl. 9), 133-137.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 133-137
-
-
Xu, J.1
Peng, J.2
Zhao, F.3
-
35
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
36
-
-
38549173606
-
The BioGRID interaction database: 2008 update
-
Breitkreutz,B.J., Stark,C., Reguly,T., Boucher,L., Breitkreutz,A., Livstone,M., Oughtred,R., Lackner,D.H., Bahler,J., Wood,V. et al. (2008) The BioGRID interaction database: 2008 update. Nucleic Acids Res., 36, D637-D640.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Breitkreutz, B.J.1
Stark, C.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
Livstone, M.6
Oughtred, R.7
Lackner, D.H.8
Bahler, J.9
Wood, V.10
-
37
-
-
33846073818
-
MINT: the Molecular INTeraction database
-
Chatr-aryamontri,A., Ceol,A., Palazzi,L., Nardelli,G., Schneider,M., Castagnoli,L. and Cesareni,G. (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res., 35, D572-D574.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Chatr-aryamontri, A.1
Ceol, A.2
Palazzi, L.3
Nardelli, G.4
Schneider, M.5
Castagnoli, L.6
Cesareni, G.7
-
38
-
-
33747853260
-
APID: Agile Protein interaction data analyzer
-
Prieto,C. and De Las Rivas,J. (2006) APID: Agile Protein interaction data analyzer. Nucleic Acids Res., 34, W298-W302.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Prieto, C.1
De Las Rivas, J.2
-
39
-
-
53749101674
-
Optimal contact map alignment of protein-protein interfaces
-
Pulim,V., Berger,B. and Bienkowska,J. (2008) Optimal contact map alignment of protein-protein interfaces. Bioinformatics, 24, 2324-2328.
-
(2008)
Bioinformatics
, vol.24
, pp. 2324-2328
-
-
Pulim, V.1
Berger, B.2
Bienkowska, J.3
-
40
-
-
38649114648
-
LTHREADER: prediction of extracellular ligand-receptor interactions in cytokines using localized threading
-
Pulim,V., Bienkowska,J. and Berger,B. (2008) LTHREADER: prediction of extracellular ligand-receptor interactions in cytokines using localized threading. Prot. Sci., 17, 279-292.
-
(2008)
Prot. Sci.
, vol.17
, pp. 279-292
-
-
Pulim, V.1
Bienkowska, J.2
Berger, B.3
|