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Volumn 7, Issue 11, 2012, Pages

PROSPER: An Integrated Feature-Based Tool for Predicting Protease Substrate Cleavage Sites

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINASE;

EID: 84870484133     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0050300     Document Type: Article
Times cited : (246)

References (96)
  • 1
    • 0036302814 scopus 로고    scopus 로고
    • Protease degradomics: a new challenge for proteomics,
    • López-Otín C, Overall CM, (2002) Protease degradomics: a new challenge for proteomics,. Nat Rev Mol Cell Biol 3: 509-519.
    • (2002) Nat Rev Mol Cell Biol , vol.3 , pp. 509-519
    • López-Otín, C.1    Overall, C.M.2
  • 2
    • 33748308883 scopus 로고    scopus 로고
    • Targeting proteases: successes, failures and future prospects
    • Turk B, (2006) Targeting proteases: successes, failures and future prospects. Nat Rev Drug Discov 5: 785-799.
    • (2006) Nat Rev Drug Discov , vol.5 , pp. 785-799
    • Turk, B.1
  • 3
    • 34648815810 scopus 로고    scopus 로고
    • Emerging roles of proteases in tumour suppression
    • López-Otín C, Matrisian LM, (2007) Emerging roles of proteases in tumour suppression. Nat Rev Cancer 7: 800-808.
    • (2007) Nat Rev Cancer , vol.7 , pp. 800-808
    • López-Otín, C.1    Matrisian, L.M.2
  • 8
  • 11
    • 35448974535 scopus 로고    scopus 로고
    • Proteome-wide identification of family member-specific natural substrate repertoire of caspases
    • Ju W, Valencia CA, Pang H, Ke Y, Gao W, et al. (2007) Proteome-wide identification of family member-specific natural substrate repertoire of caspases. Proc Natl Acad Sci USA 104: 14294-14299.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 14294-14299
    • Ju, W.1    Valencia, C.A.2    Pang, H.3    Ke, Y.4    Gao, W.5
  • 12
    • 34547191179 scopus 로고    scopus 로고
    • Identification of proteolytic cleavage sites by quantitative proteomics
    • Enoksson M, Li J, Ivancic MM, Timmer JC, Wildfang E, et al. (2007) Identification of proteolytic cleavage sites by quantitative proteomics. J Proteome Res 6: 2850-2858.
    • (2007) J Proteome Res , vol.6 , pp. 2850-2858
    • Enoksson, M.1    Li, J.2    Ivancic, M.M.3    Timmer, J.C.4    Wildfang, E.5
  • 13
    • 49549113643 scopus 로고    scopus 로고
    • Global mapping of the topography and magnitude of proteolytic events in apoptosis
    • Dix MM, Simon GM, Cravatt BF, (2008) Global mapping of the topography and magnitude of proteolytic events in apoptosis. Cell 134: 679-691.
    • (2008) Cell , vol.134 , pp. 679-691
    • Dix, M.M.1    Simon, G.M.2    Cravatt, B.F.3
  • 14
    • 52649141086 scopus 로고    scopus 로고
    • Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini
    • Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, et al. (2008) Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell 134: 866-876.
    • (2008) Cell , vol.134 , pp. 866-876
    • Mahrus, S.1    Trinidad, J.C.2    Barkan, D.T.3    Sali, A.4    Burlingame, A.L.5
  • 15
    • 44949142150 scopus 로고    scopus 로고
    • Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites
    • Schilling O, Overall CM, (2008) Proteome-derived, database-searchable peptide libraries for identifying protease cleavage sites. Nat Biotechnol 26: 685-694.
    • (2008) Nat Biotechnol , vol.26 , pp. 685-694
    • Schilling, O.1    Overall, C.M.2
  • 16
    • 75149167437 scopus 로고    scopus 로고
    • Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity
    • Demon D, Van Damme P, Vanden Berghe T, Deceuninck A, Van Durme J, et al. (2009) Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity. Mol Cell Proteomics 8: 2700-2714.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 2700-2714
    • Demon, D.1    van Damme, P.2    Vanden Berghe, T.3    Deceuninck, A.4    van Durme, J.5
  • 17
    • 61649102448 scopus 로고    scopus 로고
    • Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs
    • Van Damme P, Maurer-Stroh S, Plasman K, Van Durme J, Colaert N, et al. (2009) Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs. Mol Cell Proteomics 8: 258-272.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 258-272
    • van Damme, P.1    Maurer-Stroh, S.2    Plasman, K.3    van Durme, J.4    Colaert, N.5
  • 18
    • 77954694885 scopus 로고    scopus 로고
    • Complementary positional proteomics for screening substrates of endo- and exoproteases
    • Van Damme P, Staes A, Bronsoms S, Helsens K, Colaert N, et al. (2010) Complementary positional proteomics for screening substrates of endo- and exoproteases. Nat Methods 7: 512-515.
    • (2010) Nat Methods , vol.7 , pp. 512-515
    • van Damme, P.1    Staes, A.2    Bronsoms, S.3    Helsens, K.4    Colaert, N.5
  • 19
    • 77954693076 scopus 로고    scopus 로고
    • Proteome-wide analysis of protein carboxy termini: C terminomics
    • Schilling O, Barré O, Huesgen PF, Overall CM, (2010) Proteome-wide analysis of protein carboxy termini: C terminomics. Nat Methods 7: 508-511.
    • (2010) Nat Methods , vol.7 , pp. 508-511
    • Schilling, O.1    Barré, O.2    Huesgen, P.F.3    Overall, C.M.4
  • 20
    • 77749320923 scopus 로고    scopus 로고
    • Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products
    • Kleifeld O, Doucet A, auf dem Keller U, Prudova A, Schilling O, et al. (2010) Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat Biotechnol 28: 281-288.
    • (2010) Nat Biotechnol , vol.28 , pp. 281-288
    • Kleifeld, O.1    Doucet, A.2    auf dem Keller, U.3    Prudova, A.4    Schilling, O.5
  • 21
    • 18744369642 scopus 로고    scopus 로고
    • Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks
    • Yang ZR, (2005) Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks. Bioinformatics 21: 1831-1837.
    • (2005) Bioinformatics , vol.21 , pp. 1831-1837
    • Yang, Z.R.1
  • 22
    • 84871967410 scopus 로고    scopus 로고
    • SVM-based prediction of caspase substrate cleavage sites
    • Wee LJ, Tan TW, Ranganathan S, (2006) SVM-based prediction of caspase substrate cleavage sites. BMC Bioinformatics 7: S14.
    • (2006) BMC Bioinformatics , vol.7
    • Wee, L.J.1    Tan, T.W.2    Ranganathan, S.3
  • 23
    • 36549063702 scopus 로고    scopus 로고
    • CASVM: web server for SVM-based prediction of caspase substrates cleavage sites
    • Wee LJ, Tan TW, Ranganathan S, (2007) CASVM: web server for SVM-based prediction of caspase substrates cleavage sites. Bioinformatics 23: 3241-3243.
    • (2007) Bioinformatics , vol.23 , pp. 3241-3243
    • Wee, L.J.1    Tan, T.W.2    Ranganathan, S.3
  • 24
    • 56649119163 scopus 로고    scopus 로고
    • Protease substrate site predictors derived from machine learning on multilevel substrate phage display data
    • Chen CT, Yang EW, Hsu HJ, Sun YK, Hsu WL, et al. (2008) Protease substrate site predictors derived from machine learning on multilevel substrate phage display data. Bioinformatics 24: 2691-2697.
    • (2008) Bioinformatics , vol.24 , pp. 2691-2697
    • Chen, C.T.1    Yang, E.W.2    Hsu, H.J.3    Sun, Y.K.4    Hsu, W.L.5
  • 27
    • 77954481626 scopus 로고    scopus 로고
    • Prediction of protease substrates using sequence and structure features
    • Barkan DT, Hostetter DR, Mahrus S, Pieper U, Wells JA, et al. (2010) Prediction of protease substrates using sequence and structure features. Bioinformatics 26: 1714-1722.
    • (2010) Bioinformatics , vol.26 , pp. 1714-1722
    • Barkan, D.T.1    Hostetter, D.R.2    Mahrus, S.3    Pieper, U.4    Wells, J.A.5
  • 28
    • 77951972791 scopus 로고    scopus 로고
    • Cascleave: towards more accurate prediction of caspase substrate cleavage sites
    • Song J, Tan H, Shen H, Mahmood K, Boyd SE, et al. (2010) Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinformatics 26: 752-760.
    • (2010) Bioinformatics , vol.26 , pp. 752-760
    • Song, J.1    Tan, H.2    Shen, H.3    Mahmood, K.4    Boyd, S.E.5
  • 31
    • 23144444029 scopus 로고    scopus 로고
    • GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences
    • Backes C, Kuentzer J, Lenhof HP, Comtesse N, Meese E, (2005) GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences. Nucleic Acids Res 33: W208-W213.
    • (2005) Nucleic Acids Res , vol.33
    • Backes, C.1    Kuentzer, J.2    Lenhof, H.P.3    Comtesse, N.4    Meese, E.5
  • 36
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A, (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 37
    • 0142179209 scopus 로고    scopus 로고
    • Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data
    • Qian J, Lin J, Luscombe NM, Yu H, Gerstein M, (2003) Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics 19: 1917-1926.
    • (2003) Bioinformatics , vol.19 , pp. 1917-1926
    • Qian, J.1    Lin, J.2    Luscombe, N.M.3    Yu, H.4    Gerstein, M.5
  • 38
    • 33646195908 scopus 로고    scopus 로고
    • Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information
    • Song J, Burrage K, Yuan Z, Huber T, (2006) Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information. BMC Bioinformatics 7: 124.
    • (2006) BMC Bioinformatics , vol.7 , pp. 124
    • Song, J.1    Burrage, K.2    Yuan, Z.3    Huber, T.4
  • 39
    • 62849118051 scopus 로고    scopus 로고
    • Computational identification of protein methylation sites through bi-profile Bayes feature extraction
    • Shao J, Xu D, Tsai SN, Wang Y, Ngai SM, (2009) Computational identification of protein methylation sites through bi-profile Bayes feature extraction. PLoS ONE 4: e4920.
    • (2009) PLoS ONE , vol.4
    • Shao, J.1    Xu, D.2    Tsai, S.N.3    Wang, Y.4    Ngai, S.M.5
  • 40
    • 0025912338 scopus 로고
    • Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors
    • Hubbard SJ, Campbell SF, Thornton JM, (1991) Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J Mol Biol 220: 507-530.
    • (1991) J Mol Biol , vol.220 , pp. 507-530
    • Hubbard, S.J.1    Campbell, S.F.2    Thornton, J.M.3
  • 41
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT, (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292: 195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 42
    • 36448960843 scopus 로고    scopus 로고
    • PFRES: protein fold classification by using evolutionary information and predicted secondary structure
    • Chen K, Kurgan L, (2007) PFRES: protein fold classification by using evolutionary information and predicted secondary structure. Bioinformatics 23: 2843-2850.
    • (2007) Bioinformatics , vol.23 , pp. 2843-2850
    • Chen, K.1    Kurgan, L.2
  • 43
    • 77956502766 scopus 로고    scopus 로고
    • Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources
    • Mizianty MJ, Stach W, Chen K, Kedarisetti KD, Disfani FM, et al. (2010) Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources. Bioinformatics 26: i489-496.
    • (2010) Bioinformatics , vol.26
    • Mizianty, M.J.1    Stach, W.2    Chen, K.3    Kedarisetti, K.D.4    Disfani, F.M.5
  • 44
    • 34547852238 scopus 로고    scopus 로고
    • Prediction of DNA-binding residues from sequence
    • Ofran Y, Mysore V, Rost B, (2007) Prediction of DNA-binding residues from sequence. Bioinformatics 23: i347-353.
    • (2007) Bioinformatics , vol.23
    • Ofran, Y.1    Mysore, V.2    Rost, B.3
  • 45
    • 34547573955 scopus 로고    scopus 로고
    • Protein-protein interaction hotspots carved into sequences
    • Ofran Y, Rost B, (2007) Protein-protein interaction hotspots carved into sequences. PLoS Comput Biol 3: e119.
    • (2007) PLoS Comput Biol , vol.3
    • Ofran, Y.1    Rost, B.2
  • 46
    • 33750378680 scopus 로고    scopus 로고
    • Predicting residue-wise contact orders in proteins by support vector regression
    • Song J, Burrage K, (2006) Predicting residue-wise contact orders in proteins by support vector regression. BMC Bioinformatics 7: 425.
    • (2006) BMC Bioinformatics , vol.7 , pp. 425
    • Song, J.1    Burrage, K.2
  • 47
    • 36549021546 scopus 로고    scopus 로고
    • Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure
    • Song J, Yuan Z, Tan H, Huber T, Burrage K, (2007) Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure. Bioinformatics 23: 3147-3154.
    • (2007) Bioinformatics , vol.23 , pp. 3147-3154
    • Song, J.1    Yuan, Z.2    Tan, H.3    Huber, T.4    Burrage, K.5
  • 48
    • 46249133956 scopus 로고    scopus 로고
    • HSEpred: predict half-sphere exposure from protein sequences
    • Song J, Tan H, Takemoto K, Akutsu T, (2008) HSEpred: predict half-sphere exposure from protein sequences. Bioinformatics 24: 1489-1497.
    • (2008) Bioinformatics , vol.24 , pp. 1489-1497
    • Song, J.1    Tan, H.2    Takemoto, K.3    Akutsu, T.4
  • 49
    • 54049091165 scopus 로고    scopus 로고
    • Sequence based residue depth prediction using evolutionary information and predicted secondary structure
    • Zhang H, Zhang T, Chen K, Shen S, Ruan J, et al. (2008) Sequence based residue depth prediction using evolutionary information and predicted secondary structure. BMC Bioinformatics 9: 388.
    • (2008) BMC Bioinformatics , vol.9 , pp. 388
    • Zhang, H.1    Zhang, T.2    Chen, K.3    Shen, S.4    Ruan, J.5
  • 50
    • 0032785021 scopus 로고    scopus 로고
    • Caspase structure, proteolytic substrates, and function during apoptotic cell death
    • Nicholson DW, (1999) Caspase structure, proteolytic substrates, and function during apoptotic cell death. Cell Death Differ 6: 1028-1042.
    • (1999) Cell Death Differ , vol.6 , pp. 1028-1042
    • Nicholson, D.W.1
  • 51
  • 52
    • 34548750953 scopus 로고    scopus 로고
    • Natively unstructured regions in proteins identified from contact predictions
    • Schlessinger A, Punta M, Rost B, (2007) Natively unstructured regions in proteins identified from contact predictions. Bioinformatics 23: 2376-2384.
    • (2007) Bioinformatics , vol.23 , pp. 2376-2384
    • Schlessinger, A.1    Punta, M.2    Rost, B.3
  • 53
    • 34547599318 scopus 로고    scopus 로고
    • Natively unstructured loops differ from other loops
    • Schlessinger A, Liu J, Rost B, (2007) Natively unstructured loops differ from other loops. PLoS Comput Biol 3: e140.
    • (2007) PLoS Comput Biol , vol.3
    • Schlessinger, A.1    Liu, J.2    Rost, B.3
  • 54
    • 70349392341 scopus 로고    scopus 로고
    • Prodepth: predict residue depth by support vector regression approach from protein sequences only
    • Song J, Tan H, Mahmood K, Law RH, Buckle AM, et al. (2009) Prodepth: predict residue depth by support vector regression approach from protein sequences only. PLoS ONE 4: e7072.
    • (2009) PLoS ONE , vol.4
    • Song, J.1    Tan, H.2    Mahmood, K.3    Law, R.H.4    Buckle, A.M.5
  • 55
    • 1542358787 scopus 로고    scopus 로고
    • Prediction and functional analysis of native disorder in proteins from the three kingdoms of life
    • Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT, (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337: 635-645.
    • (2004) J Mol Biol , vol.337 , pp. 635-645
    • Ward, J.J.1    Sodhi, J.S.2    McGuffin, L.J.3    Buxton, B.F.4    Jones, D.T.5
  • 56
    • 0002714543 scopus 로고    scopus 로고
    • Making large-Scale SVM Learning Practical
    • Edited by: Schölkopf, B., Burges, C. and Smola, A., Cambridge, MA: MIT Press
    • Joachims T (1999) Making large-Scale SVM Learning Practical. In Advances in Kernel Methods- Support Vector Learning. Edited by: Schölkopf, B., Burges, C. and Smola, A., Cambridge, MA: MIT Press.
    • (1999) Advances in Kernel Methods- Support Vector Learning
    • Joachims, T.1
  • 58
    • 78049440479 scopus 로고    scopus 로고
    • High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions
    • Agius P, Arvey A, Chang W, Noble WS, Leslie C, (2010) High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions. PLoS Comput Biol 6: e1000916.
    • (2010) PLoS Comput Biol , vol.6
    • Agius, P.1    Arvey, A.2    Chang, W.3    Noble, W.S.4    Leslie, C.5
  • 59
    • 0042034151 scopus 로고    scopus 로고
    • A new method to estimate ligand-receptor energetics
    • Bock JR, Gough DA, (2002) A new method to estimate ligand-receptor energetics. Mol Cell Proteomics 1: 904-910.
    • (2002) Mol Cell Proteomics , vol.1 , pp. 904-910
    • Bock, J.R.1    Gough, D.A.2
  • 60
    • 77953898349 scopus 로고    scopus 로고
    • Multilevel support vector regression analysis to identify condition-specific regulatory networks
    • Chen L, Xuan J, Riggins RB, Wang Y, Hoffman EP, et al. (2010) Multilevel support vector regression analysis to identify condition-specific regulatory networks. Bioinformatics 26: 1416-1422.
    • (2010) Bioinformatics , vol.26 , pp. 1416-1422
    • Chen, L.1    Xuan, J.2    Riggins, R.B.3    Wang, Y.4    Hoffman, E.P.5
  • 61
    • 0345040873 scopus 로고    scopus 로고
    • Classification and regression by randomForest
    • Liaw A, Wiener M, (2002) Classification and regression by randomForest. R news 2: 18-22.
    • (2002) R News , vol.2 , pp. 18-22
    • Liaw, A.1    Wiener, M.2
  • 62
    • 79951527638 scopus 로고    scopus 로고
    • DROP: an SVM domain linker predictor trained with optimal features selected by random forest
    • Ebina T, Toh H, Kuroda Y, (2011) DROP: an SVM domain linker predictor trained with optimal features selected by random forest. Bioinformatics 27: 487-494.
    • (2011) Bioinformatics , vol.27 , pp. 487-494
    • Ebina, T.1    Toh, H.2    Kuroda, Y.3
  • 63
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews BW, (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 405: 442-451.
    • (1975) Biochim Biophys Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1
  • 64
    • 0014211618 scopus 로고
    • On the size of the active site in proteases. I. Papain
    • Schechter I, Berger A, (1967) On the size of the active site in proteases. I. Papain. Biochem Biophys Res Commun 27: 157-162.
    • (1967) Biochem Biophys Res Commun , vol.27 , pp. 157-162
    • Schechter, I.1    Berger, A.2
  • 65
    • 0030931876 scopus 로고    scopus 로고
    • Caspases: the executioners of apoptosis
    • Cohen GM, (1997) Caspases: the executioners of apoptosis. Biochem J 326: 1-16.
    • (1997) Biochem J , vol.326 , pp. 1-16
    • Cohen, G.M.1
  • 66
    • 69249100500 scopus 로고    scopus 로고
    • Human caspases: Activation, specificity and regulation
    • Pop C, Salvesen GS, (2009) Human caspases: Activation, specificity and regulation. J Biol Chem 284: 21777-21781.
    • (2009) J Biol Chem , vol.284 , pp. 21777-21781
    • Pop, C.1    Salvesen, G.S.2
  • 67
    • 0030838164 scopus 로고    scopus 로고
    • The caspase family of cysteine proteases
    • Thornberry NA, (1997) The caspase family of cysteine proteases. Br Med Bull 53: 478-490.
    • (1997) Br Med Bull , vol.53 , pp. 478-490
    • Thornberry, N.A.1
  • 68
    • 0032539578 scopus 로고    scopus 로고
    • The structural aspects of limited proteolysis of native proteins
    • Hubbard SJ, (1998) The structural aspects of limited proteolysis of native proteins. Biochim Biophys Acta 1382: 191-206.
    • (1998) Biochim Biophys Acta , vol.1382 , pp. 191-206
    • Hubbard, S.J.1
  • 71
    • 48449088976 scopus 로고    scopus 로고
    • FFPred: an integrated feature-based function prediction server for vertebrate proteomes
    • Lobley AE, Nugent T, Orengo CA, Jones DT, (2008) FFPred: an integrated feature-based function prediction server for vertebrate proteomes. Nucleic Acids Res 36: W297-W302.
    • (2008) Nucleic Acids Res , vol.36
    • Lobley, A.E.1    Nugent, T.2    Orengo, C.A.3    Jones, D.T.4
  • 72
    • 0034867975 scopus 로고    scopus 로고
    • The protein trinity-linking function and disorder
    • Dunker AK, Obradovic Z, (2001) The protein trinity-linking function and disorder. Nat Biotechnol 19: 805-806.
    • (2001) Nat Biotechnol , vol.19 , pp. 805-806
    • Dunker, A.K.1    Obradovic, Z.2
  • 73
    • 2342473198 scopus 로고    scopus 로고
    • The importance of intrinsic disorder for protein phosphorylation
    • Dunker AK, (2004) The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res 32: 1037-1049.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1037-1049
    • Dunker, A.K.1
  • 74
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • Dyson HJ, Wright PE, (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6: 197-208.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 76
    • 57149116929 scopus 로고    scopus 로고
    • Tight regulation of unstructured proteins: from transcript synthesis to protein degradation
    • Gsponer J, Futschik ME, Teichmann SA, Babu MM, (2008) Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science 322: 1365-1368.
    • (2008) Science , vol.322 , pp. 1365-1368
    • Gsponer, J.1    Futschik, M.E.2    Teichmann, S.A.3    Babu, M.M.4
  • 77
    • 66749163093 scopus 로고    scopus 로고
    • Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data
    • Edwards YJ, Lobley AE, Pentony MM, Jones DT, (2009) Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data. Genome Biol 10: R50.
    • (2009) Genome Biol , vol.10
    • Edwards, Y.J.1    Lobley, A.E.2    Pentony, M.M.3    Jones, D.T.4
  • 78
    • 41149125082 scopus 로고    scopus 로고
    • Structural disorder serves as a weak signal for intracellular protein degradation
    • Tompa P, Prilusky J, Silman I, Sussman JL, (2008) Structural disorder serves as a weak signal for intracellular protein degradation. Proteins 71: 903-909.
    • (2008) Proteins , vol.71 , pp. 903-909
    • Tompa, P.1    Prilusky, J.2    Silman, I.3    Sussman, J.L.4
  • 79
    • 67649635978 scopus 로고    scopus 로고
    • Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity
    • Vavouri T, Semple JI, Garcia-Verdugo R, Lehner B, (2009) Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity. Cell 138: 198-208.
    • (2009) Cell , vol.138 , pp. 198-208
    • Vavouri, T.1    Semple, J.I.2    Garcia-Verdugo, R.3    Lehner, B.4
  • 80
    • 78650153738 scopus 로고    scopus 로고
    • Musite, a tool for global prediction of general and kinase-specific phosphorylation sites
    • Gao J, Thelen JJ, Dunker AK, Xu D, (2010) Musite, a tool for global prediction of general and kinase-specific phosphorylation sites. Mol Cell Proteomics 9: 2586-2600.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 2586-2600
    • Gao, J.1    Thelen, J.J.2    Dunker, A.K.3    Xu, D.4
  • 81
    • 77950878660 scopus 로고    scopus 로고
    • Improving the accuracy of predicting disulfide connectivity by feature selection
    • Zhu L, Yang J, Song JN, Chou KC, Shen HB, (2010) Improving the accuracy of predicting disulfide connectivity by feature selection. J Comput Chem 31: 1478-1485.
    • (2010) J Comput Chem , vol.31 , pp. 1478-1485
    • Zhu, L.1    Yang, J.2    Song, J.N.3    Chou, K.C.4    Shen, H.B.5
  • 82
    • 80055062088 scopus 로고    scopus 로고
    • Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach
    • Wang XF, Chen Z, Wang C, Yan RX, Zhang Z, et al. (2011) Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach. PLoS ONE 6: e26767.
    • (2011) PLoS ONE , vol.6
    • Wang, X.F.1    Chen, Z.2    Wang, C.3    Yan, R.X.4    Zhang, Z.5
  • 83
    • 84865298225 scopus 로고    scopus 로고
    • FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model
    • Wang M, Zhao XM, Takemoto K, Xu H, Li Y, et al. (2012) FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model. PLoS ONE 7: e43847.
    • (2012) PLoS ONE , vol.7
    • Wang, M.1    Zhao, X.M.2    Takemoto, K.3    Xu, H.4    Li, Y.5
  • 84
    • 3042818018 scopus 로고    scopus 로고
    • The International Protein Index: An integrated database for proteomics experiments
    • Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, et al. (2004) The International Protein Index: An integrated database for proteomics experiments. Proteomics 4: 1985-1988.
    • (2004) Proteomics , vol.4 , pp. 1985-1988
    • Kersey, P.J.1    Duarte, J.2    Williams, A.3    Karavidopoulou, Y.4    Birney, E.5
  • 85
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 86
    • 67849130563 scopus 로고    scopus 로고
    • ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
    • Chen J, Bardes EE, Aronow BJ, Jegga AG, (2009) ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res 37: W305-W311.
    • (2009) Nucleic Acids Res , vol.37
    • Chen, J.1    Bardes, E.E.2    Aronow, B.J.3    Jegga, A.G.4
  • 87
    • 70350107735 scopus 로고    scopus 로고
    • The crystal structure of caspase-6, a selective effector of axonal degeneration
    • Baumgartner R, Meder G, Briand C, Decock A, D'arcy A, et al. (2009) The crystal structure of caspase-6, a selective effector of axonal degeneration. Biochem J 423: 429-439.
    • (2009) Biochem J , vol.423 , pp. 429-439
    • Baumgartner, R.1    Meder, G.2    Briand, C.3    Decock, A.4    D'arcy, A.5
  • 88
    • 63549140862 scopus 로고    scopus 로고
    • Detection of alpha-rod protein repeats using a neural network and application to huntingtin
    • Palidwor GA, Shcherbinin S, Huska MR, Rasko T, Stelzl U, et al. (2009) Detection of alpha-rod protein repeats using a neural network and application to huntingtin. PLoS Comput Biol 5: e1000304.
    • (2009) PLoS Comput Biol , vol.5
    • Palidwor, G.A.1    Shcherbinin, S.2    Huska, M.R.3    Rasko, T.4    Stelzl, U.5
  • 89
    • 0035940412 scopus 로고    scopus 로고
    • Caspase 3-cleaved N-terminal fragments of wild-type and mutant huntingtin are present in normal and Huntington's disease brains, associate with membranes, and undergo calpain-dependent proteolysis
    • Kim YJ, Yi Y, Sapp E, Wang YM, Cuiffo B, et al. (2001) Caspase 3-cleaved N-terminal fragments of wild-type and mutant huntingtin are present in normal and Huntington's disease brains, associate with membranes, and undergo calpain-dependent proteolysis. Proc Natl Acad Sci U S A 98: 12784-12789.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 12784-12789
    • Kim, Y.J.1    Yi, Y.2    Sapp, E.3    Wang, Y.M.4    Cuiffo, B.5
  • 90
    • 48049092846 scopus 로고    scopus 로고
    • Activated caspase-6 and caspase-6-cleaved fragments of huntingtin specifically colocalize in the nucleus
    • Warby SC, Doty CN, Graham RK, Carroll JB, Yang YZ, et al. (2008) Activated caspase-6 and caspase-6-cleaved fragments of huntingtin specifically colocalize in the nucleus. Hum Mol Genet 17: 2390-2404.
    • (2008) Hum Mol Genet , vol.17 , pp. 2390-2404
    • Warby, S.C.1    Doty, C.N.2    Graham, R.K.3    Carroll, J.B.4    Yang, Y.Z.5
  • 91
    • 0030848495 scopus 로고    scopus 로고
    • Site-specific dissection of substrate recognition by thrombin
    • Vindigni A, Dang QD, Cera ED, (1997) Site-specific dissection of substrate recognition by thrombin. Nat Biotech 15: 891-895.
    • (1997) Nat Biotech , vol.15 , pp. 891-895
    • Vindigni, A.1    Dang, Q.D.2    Cera, E.D.3
  • 92
    • 67649617069 scopus 로고    scopus 로고
    • Subsite cooperativity in protease specificity
    • Ng NM, Pike RN, Boyd SE, (2009) Subsite cooperativity in protease specificity. Biol Chem 390: 401-407.
    • (2009) Biol Chem , vol.390 , pp. 401-407
    • Ng, N.M.1    Pike, R.N.2    Boyd, S.E.3
  • 93
    • 34547852262 scopus 로고    scopus 로고
    • An ensemble framework for clustering protein-protein interaction networks
    • Asur S, Ucar D, Parthasarathy S, (2007) An ensemble framework for clustering protein-protein interaction networks. Bioinformatics 23: i29-40.
    • (2007) Bioinformatics , vol.23
    • Asur, S.1    Ucar, D.2    Parthasarathy, S.3
  • 94
    • 44349192171 scopus 로고    scopus 로고
    • Prediction of disordered regions in proteins based on the meta approach
    • Ishida T, Kinoshita K, (2008) Prediction of disordered regions in proteins based on the meta approach. Bioinformatics 24: 1344-1348.
    • (2008) Bioinformatics , vol.24 , pp. 1344-1348
    • Ishida, T.1    Kinoshita, K.2
  • 95
    • 63549134757 scopus 로고    scopus 로고
    • M are better than one: an ensemble-based motif finder and its application to regulatory element prediction
    • Yanover C, Singh M, Zaslavsky E, (2009) M are better than one: an ensemble-based motif finder and its application to regulatory element prediction. Bioinformatics 25: 868-874.
    • (2009) Bioinformatics , vol.25 , pp. 868-874
    • Yanover, C.1    Singh, M.2    Zaslavsky, E.3
  • 96
    • 0025008168 scopus 로고
    • Sequence logos: a new way to display consensus sequences
    • Schneider TD, Stephens RM, (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18: 6097-6100.
    • (1990) Nucleic Acids Res , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2


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