메뉴 건너뛰기




Volumn 113, Issue 43, 2016, Pages 12180-12185

Inferring interaction partners from protein sequences

Author keywords

Coevolution; Direct coupling analysis; Maximum entropy; Paralogs; Protein protein interactions

Indexed keywords

ABC TRANSPORTER; MULTIPROTEIN COMPLEX; PROTEIN HISTIDINE KINASE; PROTEIN BINDING;

EID: 84992386849     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1606762113     Document Type: Article
Times cited : (125)

References (37)
  • 1
    • 84898648935 scopus 로고    scopus 로고
    • The binary protein-protein interaction landscape of Escherichia coli
    • Rajagopala SV, et al. (2014) The binary protein-protein interaction landscape of Escherichia coli. Nat Biotechnol 32(3):285-290.
    • (2014) Nat Biotechnol , vol.32 , Issue.3 , pp. 285-290
    • Rajagopala, S.V.1
  • 2
    • 0023660022 scopus 로고
    • Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus
    • Altschuh D, Lesk AM, Bloomer AC, Klug A (1987) Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus. J Mol Biol 193(4):693-707.
    • (1987) J Mol Biol , vol.193 , Issue.4 , pp. 693-707
    • Altschuh, D.1    Lesk, A.M.2    Bloomer, A.C.3    Klug, A.4
  • 3
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless SW, Ranganathan R (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286(5438):295-299.
    • (1999) Science , vol.286 , Issue.5438 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 4
    • 44649153450 scopus 로고    scopus 로고
    • Rewiring the specificity of two-component signal transduction systems
    • Skerker JM, et al. (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133(6):1043-1054.
    • (2008) Cell , vol.133 , Issue.6 , pp. 1043-1054
    • Skerker, J.M.1
  • 5
  • 6
    • 39149114704 scopus 로고    scopus 로고
    • Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
    • Burger L, van Nimwegen E (2008) Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Mol Syst Biol 4(1):165.
    • (2008) Mol Syst Biol , vol.4 , Issue.1 , pp. 165
    • Burger, L.1    Van Nimwegen, E.2
  • 7
    • 58549114185 scopus 로고    scopus 로고
    • Identification of direct residue contacts in protein-protein interaction by message passing
    • Weigt M, White RA, Szurmant H, Hoch JA, Hwa T (2009) Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci USA 106(1):67-72.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.1 , pp. 67-72
    • Weigt, M.1    White, R.A.2    Szurmant, H.3    Hoch, J.A.4    Hwa, T.5
  • 8
    • 11944266539 scopus 로고
    • Information theory and statistical mechanics
    • Jaynes ET (1957) Information theory and statistical mechanics. Phys Rev 106(4):620-630.
    • (1957) Phys Rev , vol.106 , Issue.4 , pp. 620-630
    • Jaynes, E.T.1
  • 9
    • 82855163967 scopus 로고    scopus 로고
    • Protein 3D structure computed from evolutionary sequence variation
    • Marks DS, et al. (2011) Protein 3D structure computed from evolutionary sequence variation. PLoS One 6(12):e28766.
    • (2011) PLoS One , vol.6 , Issue.12 , pp. e28766
    • Marks, D.S.1
  • 11
    • 84856090271 scopus 로고    scopus 로고
    • PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
    • Jones DT, Buchan DW, Cozzetto D, Pontil M (2012) PSICOV: Precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 28(2):184-190.
    • (2012) Bioinformatics , vol.28 , Issue.2 , pp. 184-190
    • Jones, D.T.1    Buchan, D.W.2    Cozzetto, D.3    Pontil, M.4
  • 12
    • 84884962856 scopus 로고    scopus 로고
    • Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis
    • Dwyer RS, Ricci DP, Colwell LJ, Silhavy TJ, Wingreen NS (2013) Predicting functionally informative mutations in Escherichia coli BamA using evolutionary covariance analysis. Genetics 195(2):443-455.
    • (2013) Genetics , vol.195 , Issue.2 , pp. 443-455
    • Dwyer, R.S.1    Ricci, D.P.2    Colwell, L.J.3    Silhavy, T.J.4    Wingreen, N.S.5
  • 13
    • 84893476565 scopus 로고    scopus 로고
    • Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information
    • Cheng RR, Morcos F, Levine H, Onuchic JN (2014) Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. Proc Natl Acad Sci USA 111(5):E563-E571.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.5 , pp. E563-E571
    • Cheng, R.R.1    Morcos, F.2    Levine, H.3    Onuchic, J.N.4
  • 14
    • 84964778227 scopus 로고    scopus 로고
    • Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1
    • Figliuzzi M, Jacquier H, Schug A, Tenaillon O, Weigt M (2016) Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1. Mol Biol Evol 33(1):268-280.
    • (2016) Mol Biol Evol , vol.33 , Issue.1 , pp. 268-280
    • Figliuzzi, M.1    Jacquier, H.2    Schug, A.3    Tenaillon, O.4    Weigt, M.5
  • 15
    • 79955792165 scopus 로고    scopus 로고
    • Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: Orphans and crosstalks
    • Procaccini A, Lunt B, Szurmant H, Hwa T, Weigt M (2011) Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: Orphans and crosstalks. PLoS One 6(5):e19729.
    • (2011) PLoS One , vol.6 , Issue.5 , pp. e19729
    • Procaccini, A.1    Lunt, B.2    Szurmant, H.3    Hwa, T.4    Weigt, M.5
  • 16
    • 84899707813 scopus 로고    scopus 로고
    • Fast and accurate multivariate Gaussian modeling of protein families: Predicting residue contacts and protein-interaction partners
    • Baldassi C, et al. (2014) Fast and accurate multivariate Gaussian modeling of protein families: Predicting residue contacts and protein-interaction partners. PLoS One 9(3):e92721.
    • (2014) PLoS One , vol.9 , Issue.3 , pp. e92721
    • Baldassi, C.1
  • 17
    • 84899847547 scopus 로고    scopus 로고
    • Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information
    • Ovchinnikov S, Kamisetty H, Baker D (2014) Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. eLife 3:e02030.
    • (2014) ELife , vol.3 , pp. e02030
    • Ovchinnikov, S.1    Kamisetty, H.2    Baker, D.3
  • 18
    • 84994885238 scopus 로고    scopus 로고
    • Sequence co-evolution gives 3D contacts and structures of protein complexes
    • Hopf TA, et al. (2014) Sequence co-evolution gives 3D contacts and structures of protein complexes. eLife 3:e03430.
    • (2014) ELife , vol.3 , pp. e03430
    • Hopf, T.A.1
  • 19
    • 84979075989 scopus 로고    scopus 로고
    • Inter-protein sequence co-evolution predicts known physical interactions in bacterial ribosomes and the Trp operon
    • Feinauer C, Szurmant H, Weigt M, Pagnani A (2016) Inter-protein sequence co-evolution predicts known physical interactions in bacterial ribosomes and the Trp operon. PLoS One 11(2):e0149166.
    • (2016) PLoS One , vol.11 , Issue.2 , pp. e0149166
    • Feinauer, C.1    Szurmant, H.2    Weigt, M.3    Pagnani, A.4
  • 20
    • 33646170322 scopus 로고    scopus 로고
    • Weak pairwise correlations imply strongly correlated network states in a neural population
    • Schneidman E, Berry MJ, 2nd, Segev R, Bialek W (2006) Weak pairwise correlations imply strongly correlated network states in a neural population. Nature 440(7087):1007-1012.
    • (2006) Nature , vol.440 , Issue.7087 , pp. 1007-1012
    • Schneidman, E.1    Berry, M.J.2    Segev, R.3    Bialek, W.4
  • 21
    • 35548985891 scopus 로고    scopus 로고
    • Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns
    • Lezon TR, Banavar JR, Cieplak M, Maritan A, Fedoroff NV (2006) Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns. Proc Natl Acad Sci USA 103(50):19033-19038.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.50 , pp. 19033-19038
    • Lezon, T.R.1    Banavar, J.R.2    Cieplak, M.3    Maritan, A.4    Fedoroff, N.V.5
  • 23
    • 84859455508 scopus 로고    scopus 로고
    • Statistical mechanics for natural flocks of birds
    • Bialek W, et al. (2012) Statistical mechanics for natural flocks of birds. Proc Natl Acad Sci USA 109(13):4786-4791.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.13 , pp. 4786-4791
    • Bialek, W.1
  • 24
    • 84864369297 scopus 로고    scopus 로고
    • Mechanism-independent method for predicting response to multidrug combinations in bacteria
    • Wood K, Nishida S, Sontag ED, Cluzel P (2012) Mechanism-independent method for predicting response to multidrug combinations in bacteria. Proc Natl Acad Sci USA 109(30):12254-12259.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.30 , pp. 12254-12259
    • Wood, K.1    Nishida, S.2    Sontag, E.D.3    Cluzel, P.4
  • 25
    • 84875546274 scopus 로고    scopus 로고
    • Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design
    • Ferguson AL, et al. (2013) Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design. Immunity 38(3):606-617.
    • (2013) Immunity , vol.38 , Issue.3 , pp. 606-617
    • Ferguson, A.L.1
  • 26
    • 84923177364 scopus 로고    scopus 로고
    • The fitness landscape of HIV-1 gag: Advanced modeling approaches and validation of model predictions by in vitro testing
    • Mann JK, et al. (2014) The fitness landscape of HIV-1 gag: Advanced modeling approaches and validation of model predictions by in vitro testing. PLOS Comput Biol 10(8):e1003776.
    • (2014) PLOS Comput Biol , vol.10 , Issue.8 , pp. e1003776
    • Mann, J.K.1
  • 27
    • 70349795241 scopus 로고    scopus 로고
    • Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction
    • Casino P, Rubio V, Marina A (2009) Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction. Cell 139(2):325-336.
    • (2009) Cell , vol.139 , Issue.2 , pp. 325-336
    • Casino, P.1    Rubio, V.2    Marina, A.3
  • 28
    • 44449112421 scopus 로고    scopus 로고
    • Specificity in two-component signal transduction pathways
    • Laub MT, Goulian M (2007) Specificity in two-component signal transduction pathways. Annu Rev Genet 41:121-145.
    • (2007) Annu Rev Genet , vol.41 , pp. 121-145
    • Laub, M.T.1    Goulian, M.2
  • 29
    • 83755178457 scopus 로고    scopus 로고
    • Direct-coupling analysis of residue coevolution captures native contacts across many protein families
    • Morcos F, et al. (2011) Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci USA 108(49):E1293-E1301.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.49 , pp. E1293-E1301
    • Morcos, F.1
  • 30
    • 84975833219 scopus 로고    scopus 로고
    • Benchmarking inverse statistical approaches for protein structure and design with exactly solvable models
    • Jacquin H, Gilson A, Shakhnovich E, Cocco S, Monasson R (2016) Benchmarking inverse statistical approaches for protein structure and design with exactly solvable models. PLOS Comput Biol 12(5):e1004889.
    • (2016) PLOS Comput Biol , vol.12 , Issue.5 , pp. e1004889
    • Jacquin, H.1    Gilson, A.2    Shakhnovich, E.3    Cocco, S.4    Monasson, R.5
  • 32
    • 0004289096 scopus 로고
    • trans Pevear R, Volokhonsky L Penguin, New York
    • Tolstoy L (1877) Anna Karenina. trans Pevear R, Volokhonsky L (2001) (Penguin, New York).
    • (1877) Anna Karenina
    • Tolstoy, L.1
  • 33
    • 82255190555 scopus 로고    scopus 로고
    • Aligning graphs and finding substructures by a cavity approach
    • Bradde S, et al. (2010) Aligning graphs and finding substructures by a cavity approach. EPL 89(3):37009.
    • (2010) EPL , vol.89 , Issue.3 , pp. 37009
    • Bradde, S.1
  • 35
    • 84976865403 scopus 로고    scopus 로고
    • The Pfam protein families database: Towards a more sustainable future
    • Finn RD, et al. (2016) The Pfam protein families database: Towards a more sustainable future. Nucleic Acids Res 44(D1):D279-D285.
    • (2016) Nucleic Acids Res , vol.44 , Issue.D1 , pp. D279-D285
    • Finn, R.D.1
  • 36
    • 68049092764 scopus 로고    scopus 로고
    • P2CS: A two-component system resource for prokaryotic signal transduction research
    • Barakat M, et al. (2009) P2CS: A two-component system resource for prokaryotic signal transduction research. BMC Genomics 10:315.
    • (2009) BMC Genomics , vol.10 , pp. 315
    • Barakat, M.1
  • 37


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.