메뉴 건너뛰기




Volumn 11, Issue 5, 2015, Pages

Predicting Peptide-Mediated Interactions on a Genome-Wide Scale

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN NETWORKS; FORECASTING;

EID: 84930606332     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004248     Document Type: Article
Times cited : (15)

References (53)
  • 1
    • 77957242540 scopus 로고    scopus 로고
    • It's the machine that matters: Predicting gene function and phenotype from protein networks
    • Wang PI, Marcotte EM, It's the machine that matters: Predicting gene function and phenotype from protein networks. J Proteomics. 2010;73: 2277–2289. doi: 10.1016/j.jprot.2010.07.005 20637909
    • (2010) J Proteomics , vol.73 , pp. 2277-2289
    • Wang, P.I.1    Marcotte, E.M.2
  • 2
    • 84862703457 scopus 로고    scopus 로고
    • Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays
    • Braun P, Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays. Proteomics. 2012;12: 1499–1518. doi: 10.1002/pmic.201100598 22589225
    • (2012) Proteomics , vol.12 , pp. 1499-1518
    • Braun, P.1
  • 3
    • 1542345539 scopus 로고    scopus 로고
    • Increasing specificity in high-throughput yeast two-hybrid experiments
    • Vidalain PO, Boxem M, Ge H, Li S, Vidal M, Increasing specificity in high-throughput yeast two-hybrid experiments. Methods. 2004;32: 363–370. 15003598
    • (2004) Methods , vol.32 , pp. 363-370
    • Vidalain, P.O.1    Boxem, M.2    Ge, H.3    Li, S.4    Vidal, M.5
  • 4
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 2002;417: 399–403. 12000970
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6
  • 5
    • 0037432528 scopus 로고    scopus 로고
    • How reliable are experimental protein-protein interaction data?
    • Sprinzak E, Sattath S, Margalit H, How reliable are experimental protein-protein interaction data? J Mol Biol. 2003;327: 919–923. 12662919
    • (2003) J Mol Biol , vol.327 , pp. 919-923
    • Sprinzak, E.1    Sattath, S.2    Margalit, H.3
  • 6
    • 34247586171 scopus 로고    scopus 로고
    • Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners
    • Shoemaker BA, Panchenko AR, Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol. 2007;3: e43. 17465672
    • (2007) PLoS Comput Biol , vol.3 , pp. e43
    • Shoemaker, B.A.1    Panchenko, A.R.2
  • 7
    • 84901979488 scopus 로고    scopus 로고
    • Structural bioinformatics of the interactome
    • Petrey D, Honig B, Structural bioinformatics of the interactome. Annu Rev Biophys. 2014;43: 193–210. doi: 10.1146/annurev-biophys-051013-022726 24895853
    • (2014) Annu Rev Biophys , vol.43 , pp. 193-210
    • Petrey, D.1    Honig, B.2
  • 8
    • 0035211290 scopus 로고    scopus 로고
    • Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs"
    • Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, et al. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res. 2001;11: 2120–2126. 11731503
    • (2001) Genome Res , vol.11 , pp. 2120-2126
    • Matthews, L.R.1    Vaglio, P.2    Reboul, J.3    Ge, H.4    Davis, B.P.5    Garrels, J.6
  • 9
    • 84875225476 scopus 로고    scopus 로고
    • Emerging methods in protein co-evolution
    • de Juan D, Pazos F, Valencia A, Emerging methods in protein co-evolution. Nat Rev Genet. 2013;14: 249–261. doi: 10.1038/nrg3414 23458856
    • (2013) Nat Rev Genet , vol.14 , pp. 249-261
    • de Juan, D.1    Pazos, F.2    Valencia, A.3
  • 10
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: a fingerprint of proteins that physically interact
    • Dandekar T, Snel B, Huynen M, Bork P, Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci. 1998;23: 324–328. 9787636
    • (1998) Trends Biochem Sci , vol.23 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 11
    • 33847064282 scopus 로고    scopus 로고
    • Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
    • Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, et al. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol. 2006;5: 11. 16762047
    • (2006) J Biol , vol.5 , pp. 11
    • Reguly, T.1    Breitkreutz, A.2    Boucher, L.3    Breitkreutz, B.J.4    Hon, G.C.5    Myers, C.L.6
  • 12
    • 84871967106 scopus 로고    scopus 로고
    • Interactome3D: adding structural details to protein networks
    • Mosca R, Ceol A, Aloy P, Interactome3D: adding structural details to protein networks. Nat Methods. 2013;10: 47–53. doi: 10.1038/nmeth.2289 23399932
    • (2013) Nat Methods , vol.10 , pp. 47-53
    • Mosca, R.1    Ceol, A.2    Aloy, P.3
  • 13
    • 84867881743 scopus 로고    scopus 로고
    • Structure-based prediction of protein-protein interactions on a genome-wide scale
    • Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, et al. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature. 2012;490: 556–560. doi: 10.1038/nature11503 23023127
    • (2012) Nature , vol.490 , pp. 556-560
    • Zhang, Q.C.1    Petrey, D.2    Deng, L.3    Qiang, L.4    Shi, Y.5    Thu, C.A.6
  • 14
    • 84876515907 scopus 로고    scopus 로고
    • STRING v9.1: protein-protein interaction networks, with increased coverage and integration
    • Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013;41: D808–D815. doi: 10.1093/nar/gks1094 23203871
    • (2013) Nucleic Acids Res , vol.41 , pp. D808-D815
    • Franceschini, A.1    Szklarczyk, D.2    Frankild, S.3    Kuhn, M.4    Simonovic, M.5    Roth, A.6
  • 15
    • 0037453510 scopus 로고    scopus 로고
    • Assembly of cell regulatory systems through protein interaction domains
    • Pawson T, Nash P, Assembly of cell regulatory systems through protein interaction domains. Science. 2003;300: 445–452. 12702867
    • (2003) Science , vol.300 , pp. 445-452
    • Pawson, T.1    Nash, P.2
  • 16
    • 49549083915 scopus 로고    scopus 로고
    • Peptide-mediated interactions in biological systems: new discoveries and applications
    • Petsalaki E, Russell RB, Peptide-mediated interactions in biological systems: new discoveries and applications. Curr Opin Biotechnol. 2008;19: 344–350. doi: 10.1016/j.copbio.2008.06.004 18602004
    • (2008) Curr Opin Biotechnol , vol.19 , pp. 344-350
    • Petsalaki, E.1    Russell, R.B.2
  • 17
    • 84904469894 scopus 로고    scopus 로고
    • A million peptide motifs for the molecular biologist
    • Tompa P, Davey NE, Gibson TJ, Babu MM, A million peptide motifs for the molecular biologist. Mol Cell. 2014;55: 161–169. doi: 10.1016/j.molcel.2014.05.032 25038412
    • (2014) Mol Cell , vol.55 , pp. 161-169
    • Tompa, P.1    Davey, N.E.2    Gibson, T.J.3    Babu, M.M.4
  • 18
    • 84902446852 scopus 로고    scopus 로고
    • Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation
    • Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, et al. Short linear motifs: ubiquitous and functionally diverse protein interaction modules directing cell regulation. Chem Rev. 2014;114: 6733–6778. doi: 10.1021/cr400585q 24926813
    • (2014) Chem Rev , vol.114 , pp. 6733-6778
    • Van Roey, K.1    Uyar, B.2    Weatheritt, R.J.3    Dinkel, H.4    Seiler, M.5    Budd, A.6
  • 19
    • 84862642911 scopus 로고    scopus 로고
    • High-throughput analysis of peptide-binding modules
    • Liu BA, Engelmann BW, Nash PD, High-throughput analysis of peptide-binding modules. Proteomics. 2012;12: 1527–1546. doi: 10.1002/pmic.201100599 22610655
    • (2012) Proteomics , vol.12 , pp. 1527-1546
    • Liu, B.A.1    Engelmann, B.W.2    Nash, P.D.3
  • 20
    • 70350404403 scopus 로고    scopus 로고
    • Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins
    • Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, et al. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol. 2009;7: e1000218. doi: 10.1371/journal.pbio.1000218 19841731
    • (2009) PLoS Biol , vol.7 , pp. e1000218
    • Tonikian, R.1    Xin, X.2    Toret, C.P.3    Gfeller, D.4    Landgraf, C.5    Panni, S.6
  • 22
    • 51349085386 scopus 로고    scopus 로고
    • Predicting PDZ domain-peptide interactions from primary sequences
    • Chen JR, Chang BH, Allen JE, Stiffler MA, MacBeath G, Predicting PDZ domain-peptide interactions from primary sequences. Nat Biotechnol. 2008;26: 1041–1045. doi: 10.1038/nbt.1489 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
  • 23
    • 33645776269 scopus 로고    scopus 로고
    • Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain
    • Hou T, Chen K, McLaughlin WA, Lu B, Wang W, Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Comput Biol. 2006;2: e1. 16446784
    • (2006) PLoS Comput Biol , vol.2 , pp. e1
    • Hou, T.1    Chen, K.2    McLaughlin, W.A.3    Lu, B.4    Wang, W.5
  • 24
    • 42949092832 scopus 로고    scopus 로고
    • Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm
    • Sanchez IE, Beltrao P, Stricher F, Schymkowitz J, Ferkinghoff-Borg J, Rousseau F, et al. Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm. PLoS Comput Biol. 2008;4: e1000052. doi: 10.1371/journal.pcbi.1000052 18389064
    • (2008) PLoS Comput Biol , vol.4 , pp. e1000052
    • Sanchez, I.E.1    Beltrao, P.2    Stricher, F.3    Schymkowitz, J.4    Ferkinghoff-Borg, J.5    Rousseau, F.6
  • 25
    • 80055068044 scopus 로고    scopus 로고
    • Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity
    • London N, Lamphear CL, Hougland JL, Fierke CA, Schueler-Furman O, Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity. PLoS Comput Biol. 2011;7: e1002170. doi: 10.1371/journal.pcbi.1002170 21998565
    • (2011) PLoS Comput Biol , vol.7 , pp. e1002170
    • London, N.1    Lamphear, C.L.2    Hougland, J.L.3    Fierke, C.A.4    Schueler-Furman, O.5
  • 26
    • 84903397360 scopus 로고    scopus 로고
    • Genome-wide prediction and validation of peptides that bind human prosurvival Bcl-2 proteins
    • DeBartolo J, Taipale M, Keating AE, Genome-wide prediction and validation of peptides that bind human prosurvival Bcl-2 proteins. PLoS Comput Biol. 2014;10: e1003693. doi: 10.1371/journal.pcbi.1003693 24967846
    • (2014) PLoS Comput Biol , vol.10 , pp. e1003693
    • DeBartolo, J.1    Taipale, M.2    Keating, A.E.3
  • 27
    • 84864579478 scopus 로고    scopus 로고
    • Domain-mediated protein interaction prediction: From genome to network
    • Reimand J, Hui S, Jain S, Law B, Bader GD, Domain-mediated protein interaction prediction: From genome to network. FEBS Lett. 2012;586: 2751–2763. doi: 10.1016/j.febslet.2012.04.027 22561014
    • (2012) FEBS Lett , vol.586 , pp. 2751-2763
    • Reimand, J.1    Hui, S.2    Jain, S.3    Law, B.4    Bader, G.D.5
  • 29
    • 84859225975 scopus 로고    scopus 로고
    • The identification of short linear motif-mediated interfaces within the human interactome
    • Weatheritt RJ, Luck K, Petsalaki E, Davey NE, Gibson TJ, The identification of short linear motif-mediated interfaces within the human interactome. Bioinformatics. 2012;28: 976–982. doi: 10.1093/bioinformatics/bts072 22328783
    • (2012) Bioinformatics , vol.28 , pp. 976-982
    • Weatheritt, R.J.1    Luck, K.2    Petsalaki, E.3    Davey, N.E.4    Gibson, T.J.5
  • 30
    • 77955476975 scopus 로고    scopus 로고
    • Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures
    • Stein A, Aloy P, Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures. PLoS Comput Biol. 2010;6: e1000789. doi: 10.1371/journal.pcbi.1000789 20502673
    • (2010) PLoS Comput Biol , vol.6 , pp. e1000789
    • Stein, A.1    Aloy, P.2
  • 31
    • 75849126506 scopus 로고    scopus 로고
    • The structural basis of peptide-protein binding strategies
    • London N, Movshovitz-Attias D, Schueler-Furman O, The structural basis of peptide-protein binding strategies. Structure. 2010;18: 188–199. doi: 10.1016/j.str.2009.11.012 20159464
    • (2010) Structure , vol.18 , pp. 188-199
    • London, N.1    Movshovitz-Attias, D.2    Schueler-Furman, O.3
  • 32
    • 34249695447 scopus 로고    scopus 로고
    • Local structural disorder imparts plasticity on linear motifs
    • Fuxreiter M, Tompa P, Simon I, Local structural disorder imparts plasticity on linear motifs. Bioinformatics. 2007;23: 950–956. 17387114
    • (2007) Bioinformatics , vol.23 , pp. 950-956
    • Fuxreiter, M.1    Tompa, P.2    Simon, I.3
  • 33
    • 43249115776 scopus 로고    scopus 로고
    • A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences
    • Chica C, Labarga A, Gould CM, Lopez R, Gibson TJ, A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. BMC Bioinformatics. 2008;9: 229. doi: 10.1186/1471-2105-9-229 18460207
    • (2008) BMC Bioinformatics , vol.9 , pp. 229
    • Chica, C.1    Labarga, A.2    Gould, C.M.3    Lopez, R.4    Gibson, T.J.5
  • 34
  • 35
    • 33644874394 scopus 로고    scopus 로고
    • MODBASE: a database of annotated comparative protein structure models and associated resources
    • Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, et al. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2006;34: D291–D295. 16381869
    • (2006) Nucleic Acids Res , vol.34 , pp. D291-D295
    • Pieper, U.1    Eswar, N.2    Davis, F.P.3    Braberg, H.4    Madhusudhan, M.S.5    Rossi, A.6
  • 36
    • 33847069615 scopus 로고    scopus 로고
    • Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization
    • Mirkovic N, Li Z, Parnassa A, Murray D, Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization. Proteins. 2007;66: 766–777. 17154423
    • (2007) Proteins , vol.66 , pp. 766-777
    • Mirkovic, N.1    Li, Z.2    Parnassa, A.3    Murray, D.4
  • 37
    • 3543047963 scopus 로고    scopus 로고
    • Where did the BLOSUM62 alignment score matrix come from?
    • Eddy SR, Where did the BLOSUM62 alignment score matrix come from? Nat Biotechnol. 2004;22: 1035–1036. 15286655
    • (2004) Nat Biotechnol , vol.22 , pp. 1035-1036
    • Eddy, S.R.1
  • 38
    • 0142052944 scopus 로고    scopus 로고
    • A Bayesian networks approach for predicting protein-protein interactions from genomic data
    • Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, et al. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science. 2003;302: 449–453. 14564010
    • (2003) Science , vol.302 , pp. 449-453
    • Jansen, R.1    Yu, H.2    Greenbaum, D.3    Kluger, Y.4    Krogan, N.J.5    Chung, S.6
  • 39
    • 84891783174 scopus 로고    scopus 로고
    • Activities at the Universal Protein Resource (UniProt)
    • The UniProt Consortium. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2014;42: D191–D198. doi: 10.1093/nar/gkt1140 24253303
    • (2014) Nucleic Acids Res , vol.42 , pp. D191-D198
  • 41
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: interactive sequence similarity searching
    • Finn RD, Clements J, Eddy SR, HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39: W29–W37. doi: 10.1093/nar/gkr367 21593126
    • (2011) Nucleic Acids Res , vol.39 , pp. W29-W37
    • Finn, R.D.1    Clements, J.2    Eddy, S.R.3
  • 42
    • 0034682881 scopus 로고    scopus 로고
    • An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance
    • Yang AS, Honig B, An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance. J Mol Biol. 2000;301: 665–678. 10966776
    • (2000) J Mol Biol , vol.301 , pp. 665-678
    • Yang, A.S.1    Honig, B.2
  • 43
    • 0026319199 scopus 로고
    • Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls A, Sharp KA, Honig B, Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 1991;11: 281–296. 1758883
    • (1991) Proteins , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 44
    • 24044538903 scopus 로고    scopus 로고
    • IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    • Dosztanyi Z, Csizmok V, Tompa P, Simon I, IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics. 2005;21: 3433–3434. 15955779
    • (2005) Bioinformatics , vol.21 , pp. 3433-3434
    • Dosztanyi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4
  • 45
    • 34547588388 scopus 로고    scopus 로고
    • The SLiMDisc server: short, linear motif discovery in proteins
    • Davey NE, Edwards RJ, Shields DC, The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res. 2007;35: W455–W459. 17576682
    • (2007) Nucleic Acids Res , vol.35 , pp. W455-W459
    • Davey, N.E.1    Edwards, R.J.2    Shields, D.C.3
  • 46
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar RC, MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32: 1792–1797. 15034147
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 47
    • 60149099647 scopus 로고    scopus 로고
    • Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery
    • Davey NE, Shields DC, Edwards RJ, Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinformatics. 2009;25: 443–450. doi: 10.1093/bioinformatics/btn664 19136552
    • (2009) Bioinformatics , vol.25 , pp. 443-450
    • Davey, N.E.1    Shields, D.C.2    Edwards, R.J.3
  • 53
    • 33749249600 scopus 로고    scopus 로고
    • The relationship between precision-recall and ROC curves
    • Davis J, Goadrich M. The relationship between precision-recall and ROC curves. 23rd International Conference on Machine Learning (ICML). 2006.
    • (2006)
    • Davis, J.1    Goadrich, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.