-
1
-
-
0031055372
-
Evidence for PDZ domains in bacteria, yeast, and plants
-
10.1002/pro.5560060225, 2143646, 9041651
-
Ponting CP. Evidence for PDZ domains in bacteria, yeast, and plants. Protein Sci 1997, 6:464-468. 10.1002/pro.5560060225, 2143646, 9041651.
-
(1997)
Protein Sci
, vol.6
, pp. 464-468
-
-
Ponting, C.P.1
-
2
-
-
0037453510
-
Assembly of cell regulatory systems through protein interaction domains
-
10.1126/science.1083653, 12702867
-
Pawson T, Nash P. Assembly of cell regulatory systems through protein interaction domains. Science 2003, 300:445-452. 10.1126/science.1083653, 12702867.
-
(2003)
Science
, vol.300
, pp. 445-452
-
-
Pawson, T.1
Nash, P.2
-
3
-
-
10444276589
-
Making protein interactions druggable: targeting PDZ domains
-
10.1038/nrd1578, 15573103
-
Dev KK. Making protein interactions druggable: targeting PDZ domains. Nat Rev Drug Discov 2004, 3:1047-1056. 10.1038/nrd1578, 15573103.
-
(2004)
Nat Rev Drug Discov
, vol.3
, pp. 1047-1056
-
-
Dev, K.K.1
-
4
-
-
33646675570
-
Molecular biology of human papillomavirus infection and cervical cancer
-
10.1042/CS20050369, 16597322
-
Doorbar J. Molecular biology of human papillomavirus infection and cervical cancer. Clin Sci 2006, 110:525-541. 10.1042/CS20050369, 16597322.
-
(2006)
Clin Sci
, vol.110
, pp. 525-541
-
-
Doorbar, J.1
-
5
-
-
0344390884
-
A PDZ-interacting domain in CFTR is an apical membrane polarization signal
-
10.1172/JCI7453, 409842, 10562297
-
Moyer BD, Denton J, Karlson KH, Reynolds D, Wang S, Mickle JE, Milewski M, Cutting GR, Guggino WB, Li M, Stanton BA. A PDZ-interacting domain in CFTR is an apical membrane polarization signal. J Clin Invest 1999, 104:1353-1361. 10.1172/JCI7453, 409842, 10562297.
-
(1999)
J Clin Invest
, vol.104
, pp. 1353-1361
-
-
Moyer, B.D.1
Denton, J.2
Karlson, K.H.3
Reynolds, D.4
Wang, S.5
Mickle, J.E.6
Milewski, M.7
Cutting, G.R.8
Guggino, W.B.9
Li, M.10
Stanton, B.A.11
-
6
-
-
15644379801
-
Recognition of unique carboxyl-terminal motifs by distinct PDZ domains
-
10.1126/science.275.5296.73, 8974395
-
Songyang Z, Fanning AS, Fu C, Xu J, Marfatia SM, Chishti AH, Crompton A, Chan AC, Anderson JM, Cantley LC. Recognition of unique carboxyl-terminal motifs by distinct PDZ domains. Science 1997, 275:73-77. 10.1126/science.275.5296.73, 8974395.
-
(1997)
Science
, vol.275
, pp. 73-77
-
-
Songyang, Z.1
Fanning, A.S.2
Fu, C.3
Xu, J.4
Marfatia, S.M.5
Chishti, A.H.6
Crompton, A.7
Chan, A.C.8
Anderson, J.M.9
Cantley, L.C.10
-
7
-
-
54749086397
-
A specificity map for the PDZ domain family
-
10.1371/journal.pbio.0060239, 2553845, 18828675
-
Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh JH, Reva B, Held HA, Appleton BA, Evangelista M, Wu Y, et al. A specificity map for the PDZ domain family. PLoS Biol 2008, 6:e239. 10.1371/journal.pbio.0060239, 2553845, 18828675.
-
(2008)
PLoS Biol
, vol.6
-
-
Tonikian, R.1
Zhang, Y.2
Sazinsky, S.L.3
Currell, B.4
Yeh, J.H.5
Reva, B.6
Held, H.A.7
Appleton, B.A.8
Evangelista, M.9
Wu, Y.10
-
8
-
-
4744353840
-
Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides
-
10.1016/j.jmb.2004.08.064, 15465056
-
Wiedemann U, Boisguerin P, Leben R, Leitner D, Krause G, Moelling K, Volkmer-Engert R, Oschkinat H. Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides. J Mol Biol 2004, 343:703-718. 10.1016/j.jmb.2004.08.064, 15465056.
-
(2004)
J Mol Biol
, vol.343
, pp. 703-718
-
-
Wiedemann, U.1
Boisguerin, P.2
Leben, R.3
Leitner, D.4
Krause, G.5
Moelling, K.6
Volkmer-Engert, R.7
Oschkinat, H.8
-
9
-
-
34547127612
-
PDZ domain binding selectivity is optimized across the mouse proteome
-
10.1126/science.1144592, 2674608, 17641200
-
Stiffler MA, Chen JR, Grantcharova VP, Lei Y, Fuchs D, Allen JE, Zaslavskaia LA, MacBeath G. PDZ domain binding selectivity is optimized across the mouse proteome. Science 2007, 317:364-369. 10.1126/science.1144592, 2674608, 17641200.
-
(2007)
Science
, vol.317
, pp. 364-369
-
-
Stiffler, M.A.1
Chen, J.R.2
Grantcharova, V.P.3
Lei, Y.4
Fuchs, D.5
Allen, J.E.6
Zaslavskaia, L.A.7
MacBeath, G.8
-
10
-
-
0142174642
-
Prediction of MHC class I binding peptides, using SVMHC
-
10.1186/1471-2105-3-25, 129981, 12225620
-
Donnes P, Elofsson A. Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics 2002, 3:25. 10.1186/1471-2105-3-25, 129981, 12225620.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 25
-
-
Donnes, P.1
Elofsson, A.2
-
11
-
-
33644870557
-
A regularized discriminative model for the prediction of protein-peptide interactions
-
10.1093/bioinformatics/bti804, 16397010
-
Lehrach WP, Husmeier D, Williams CK. A regularized discriminative model for the prediction of protein-peptide interactions. Bioinformatics 2006, 22:532-540. 10.1093/bioinformatics/bti804, 16397010.
-
(2006)
Bioinformatics
, vol.22
, pp. 532-540
-
-
Lehrach, W.P.1
Husmeier, D.2
Williams, C.K.3
-
12
-
-
0035072833
-
A motif-based profile scanning approach for genome-wide prediction of signaling pathways
-
10.1038/86737, 11283593
-
Yaffe MB, Leparc GG, Lai J, Obata T, Volinia S, Cantley LC. A motif-based profile scanning approach for genome-wide prediction of signaling pathways. Nat Biotechnol 2001, 19:348-353. 10.1038/86737, 11283593.
-
(2001)
Nat Biotechnol
, vol.19
, pp. 348-353
-
-
Yaffe, M.B.1
Leparc, G.G.2
Lai, J.3
Obata, T.4
Volinia, S.5
Cantley, L.C.6
-
13
-
-
0037422596
-
Structural basis and prediction of substrate specificity in protein serine/threonine kinases
-
Brinkworth RI, Breinl RA, Kobe B. Structural basis and prediction of substrate specificity in protein serine/threonine kinases. P Natl Acad Sci USA 2003, 100:74-79.
-
(2003)
P Natl Acad Sci USA
, vol.100
, pp. 74-79
-
-
Brinkworth, R.I.1
Breinl, R.A.2
Kobe, B.3
-
14
-
-
69049083531
-
Using genome-wide measurements for computational prediction of SH2-peptide interactions
-
10.1093/nar/gkp394, 2724268, 19502496
-
Wunderlich Z, Mirny LA. Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Res 2009, 37:4629-4641. 10.1093/nar/gkp394, 2724268, 19502496.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 4629-4641
-
-
Wunderlich, Z.1
Mirny, L.A.2
-
15
-
-
67650281206
-
A machine learning based method for the prediction of G protein-coupled receptor-binding PDZ domain proteins
-
10.1007/s10059-009-0091-2, 19533032
-
Eo HS, Kim S, Koo H, Kim W. A machine learning based method for the prediction of G protein-coupled receptor-binding PDZ domain proteins. Mol Cells 2009, 27:629-634. 10.1007/s10059-009-0091-2, 19533032.
-
(2009)
Mol Cells
, vol.27
, pp. 629-634
-
-
Eo, H.S.1
Kim, S.2
Koo, H.3
Kim, W.4
-
16
-
-
51349085386
-
Predicting PDZ domain-peptide interactions from primary sequences
-
10.1038/nbt.1489, 2655215, 18711339
-
Chen JR, Chang BH, Allen JE, Stiffler MA, MacBeath G. Predicting PDZ domain-peptide interactions from primary sequences. Nat Biotechnol 2008, 26:1041-1045. 10.1038/nbt.1489, 2655215, 18711339.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1041-1045
-
-
Chen, J.R.1
Chang, B.H.2
Allen, J.E.3
Stiffler, M.A.4
MacBeath, G.5
-
17
-
-
15944375458
-
PDZBase: a protein-protein interaction database for PDZ-domains
-
10.1093/bioinformatics/bti098, 15513994
-
Beuming T, Skrabanek L, Niv MY, Mukherjee P, Weinstein H. PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics 2005, 21:827-828. 10.1093/bioinformatics/bti098, 15513994.
-
(2005)
Bioinformatics
, vol.21
, pp. 827-828
-
-
Beuming, T.1
Skrabanek, L.2
Niv, M.Y.3
Mukherjee, P.4
Weinstein, H.5
-
18
-
-
33947328242
-
Choosing negative examples for the prediction of protein-protein interactions
-
10.1186/1471-2105-7-S1-S2, 1810313, 16723005
-
Ben-Hur A, Noble WS. Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics 2006, 7(Suppl 1):S2. 10.1186/1471-2105-7-S1-S2, 1810313, 16723005.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL 1
-
-
Ben-Hur, A.1
Noble, W.S.2
-
19
-
-
16344384583
-
Effect of training datasets on support vector machine prediction of protein-protein interactions
-
10.1002/pmic.200401118, 15717327
-
Lo SL, Cai CZ, Chen YZ, Chung MC. Effect of training datasets on support vector machine prediction of protein-protein interactions. Proteomics 2005, 5:876-884. 10.1002/pmic.200401118, 15717327.
-
(2005)
Proteomics
, vol.5
, pp. 876-884
-
-
Lo, S.L.1
Cai, C.Z.2
Chen, Y.Z.3
Chung, M.C.4
-
21
-
-
0003798635
-
An introduction to support vector machines and other kernel-based learning methods
-
Cambridge; New York: Cambridge University Press
-
Cristianini N, Shawe-Taylor J. An introduction to support vector machines and other kernel-based learning methods. 2000, Cambridge; New York: Cambridge University Press.
-
(2000)
-
-
Cristianini, N.1
Shawe-Taylor, J.2
-
22
-
-
0003408420
-
Learning with kernels: support vector machines, regularization, optimization, and beyond
-
Cambridge, Mass.: MIT Press
-
Schölkopf B, Smola AJ. Learning with kernels: support vector machines, regularization, optimization, and beyond. 2002, Cambridge, Mass.: MIT Press.
-
(2002)
-
-
Schölkopf, B.1
Smola, A.J.2
-
23
-
-
84871670892
-
LIBSVM: a library for support vector machines
-
LIBSVM: a library for support vector machines. , http://www.csie.ntu.edu.tw/~cjlin/libsvm
-
-
-
-
25
-
-
33646023117
-
An introduction to ROC analysis
-
Fawcett T. An introduction to ROC analysis. Pattern Recogn Lett 2006, 27:861-874.
-
(2006)
Pattern Recogn Lett
, vol.27
, pp. 861-874
-
-
Fawcett, T.1
-
26
-
-
18144406581
-
Solving the protein sequence metric problem
-
Atchley WR, Zhao JP, Fernandes AD, Druke T. Solving the protein sequence metric problem. P Natl Acad Sci USA 2005, 102:6395-6400.
-
(2005)
P Natl Acad Sci USA
, vol.102
, pp. 6395-6400
-
-
Atchley, W.R.1
Zhao, J.P.2
Fernandes, A.D.3
Druke, T.4
-
27
-
-
58149185123
-
Ensembl 2009
-
10.1093/nar/gkn828, 2686571, 19033362
-
Hubbard TJP, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, et al. Ensembl 2009. Nucleic Acids Res 2009, 37:D690-D697. 10.1093/nar/gkn828, 2686571, 19033362.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Hubbard, T.J.P.1
Aken, B.L.2
Ayling, S.3
Ballester, B.4
Beal, K.5
Bragin, E.6
Brent, S.7
Chen, Y.8
Clapham, P.9
Clarke, L.10
-
28
-
-
54949127160
-
IRefIndex: A consolidated protein interaction database with provenance
-
10.1186/1471-2105-9-405, 2573892, 18823568
-
Razick S, Magklaras G, Donaldson IM. iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics 2008, 9:405. 10.1186/1471-2105-9-405, 2573892, 18823568.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 405
-
-
Razick, S.1
Magklaras, G.2
Donaldson, I.M.3
-
29
-
-
24044440971
-
BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
-
10.1093/bioinformatics/bti551, 15972284
-
Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics 2005, 21:3448-3449. 10.1093/bioinformatics/bti551, 15972284.
-
(2005)
Bioinformatics
, vol.21
, pp. 3448-3449
-
-
Maere, S.1
Heymans, K.2
Kuiper, M.3
-
30
-
-
19444365861
-
Cilia and disease
-
10.1016/j.gde.2005.04.008, 15917207
-
Eley L, Yates LM, Goodship JA. Cilia and disease. Curr Opin Genet Dev 2005, 15:308-314. 10.1016/j.gde.2005.04.008, 15917207.
-
(2005)
Curr Opin Genet Dev
, vol.15
, pp. 308-314
-
-
Eley, L.1
Yates, L.M.2
Goodship, J.A.3
-
31
-
-
0142052944
-
A Bayesian networks approach for predicting protein-protein interactions from genomic data
-
10.1126/science.1087361, 14564010
-
Jansen R, Yu HY, Greenbaum D, Kluger Y, Krogan NJ, Chung SB, Emili A, Snyder M, Greenblatt JF, Gerstein M. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 2003, 302:449-453. 10.1126/science.1087361, 14564010.
-
(2003)
Science
, vol.302
, pp. 449-453
-
-
Jansen, R.1
Yu, H.Y.2
Greenbaum, D.3
Kluger, Y.4
Krogan, N.J.5
Chung, S.B.6
Emili, A.7
Snyder, M.8
Greenblatt, J.F.9
Gerstein, M.10
-
32
-
-
46749130932
-
PRINCESS, a protein interaction confidence evaluation system with multiple data sources
-
10.1074/mcp.M700287-MCP200, 18230642
-
Li D, Liu WL, Liu ZY, Wang J, Liu QJ, Zhu YP, He FC. PRINCESS, a protein interaction confidence evaluation system with multiple data sources. Mol Cell Proteomics 2008, 7:1043-1052. 10.1074/mcp.M700287-MCP200, 18230642.
-
(2008)
Mol Cell Proteomics
, vol.7
, pp. 1043-1052
-
-
Li, D.1
Liu, W.L.2
Liu, Z.Y.3
Wang, J.4
Liu, Q.J.5
Zhu, Y.P.6
He, F.C.7
-
33
-
-
33749511033
-
Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study
-
Basdevant N, Weinstein H, Ceruso M. Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study. J Am ChemSoc 2006, 128:12766-12777.
-
(2006)
J Am ChemSoc
, vol.128
, pp. 12766-12777
-
-
Basdevant, N.1
Weinstein, H.2
Ceruso, M.3
-
34
-
-
0347753736
-
Ligand-dependent dynamics and intramolecular signaling in a PDZ domain
-
10.1016/j.jmb.2003.11.010, 14698303
-
Fuentes EJ, Der CJ, Lee AL. Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. J Mol Biol 2004, 335:1105-1115. 10.1016/j.jmb.2003.11.010, 14698303.
-
(2004)
J Mol Biol
, vol.335
, pp. 1105-1115
-
-
Fuentes, E.J.1
Der, C.J.2
Lee, A.L.3
-
35
-
-
77952305592
-
Large-scale prediction of protein-protein interactions from structures
-
10.1186/1471-2105-11-144, 2842260, 20196863
-
Hue M, Riffle M, Vert JP, Noble WS. Large-scale prediction of protein-protein interactions from structures. BMC Bioinformatics 2010, 11:114. 10.1186/1471-2105-11-144, 2842260, 20196863.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 114
-
-
Hue, M.1
Riffle, M.2
Vert, J.P.3
Noble, W.S.4
|