메뉴 건너뛰기




Volumn 7, Issue 9, 2012, Pages

Prediction of Protein Cleavage Site with Feature Selection by Random Forest

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; BIOCHEMISTRY; GENETIC CONSERVATION; INCREMENTAL FEATURE SELECTION; INTERMETHOD COMPARISON; LEARNING ALGORITHM; MAXIMUM RELEVANCE MINIMUM REDUNDANCY METHOD; PHYSICAL CHEMISTRY; PREDICTIVE VALUE; PREDICTOR VARIABLE; PROCESS DEVELOPMENT; PROTEIN ANALYSIS; PROTEIN CLEAVAGE; PROTEIN SECONDARY STRUCTURE; RANDOM FOREST; VALIDATION PROCESS;

EID: 84866513535     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0045854     Document Type: Article
Times cited : (50)

References (43)
  • 5
    • 44649155073 scopus 로고    scopus 로고
    • Disentanglement of protease substrate repertoires
    • Van Damme P, Vandekerckhove J, Gevaert K, (2008) Disentanglement of protease substrate repertoires. Biol Chem 389: 371-381.
    • (2008) Biol Chem , vol.389 , pp. 371-381
    • van Damme, P.1    Vandekerckhove, J.2    Gevaert, K.3
  • 7
    • 0345291184 scopus 로고    scopus 로고
    • A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20 S proteasome
    • Holzhutter HG, Frommel C, Kloetzel PM, (1999) A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20 S proteasome. J Mol Biol 286: 1251-1265.
    • (1999) J Mol Biol , vol.286 , pp. 1251-1265
    • Holzhutter, H.G.1    Frommel, C.2    Kloetzel, P.M.3
  • 8
    • 0033849945 scopus 로고    scopus 로고
    • A kinetic model of vertebrate 20S proteasome accounting for the generation of major proteolytic fragments from oligomeric peptide substrates
    • Holzhutter HG, Kloetzel PM, (2000) A kinetic model of vertebrate 20S proteasome accounting for the generation of major proteolytic fragments from oligomeric peptide substrates. Biophys J 79: 1196-1205.
    • (2000) Biophys J , vol.79 , pp. 1196-1205
    • Holzhutter, H.G.1    Kloetzel, P.M.2
  • 9
    • 17844385106 scopus 로고    scopus 로고
    • The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage
    • Nielsen M, Lundegaard C, Lund O, Kesmir C, (2005) The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics 57: 33-41.
    • (2005) Immunogenetics , vol.57 , pp. 33-41
    • Nielsen, M.1    Lundegaard, C.2    Lund, O.3    Kesmir, C.4
  • 10
    • 79955395083 scopus 로고    scopus 로고
    • GPS-CCD: a novel computational program for the prediction of calpain cleavage sites
    • Liu Z, Cao J, Gao X, Ma Q, Ren J, et al. (2011) GPS-CCD: a novel computational program for the prediction of calpain cleavage sites. PLoS One 6: e19001.
    • (2011) PLoS One , vol.6
    • Liu, Z.1    Cao, J.2    Gao, X.3    Ma, Q.4    Ren, J.5
  • 11
    • 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: W208-213.
    • (2005) Nucleic Acids Res , vol.33
    • Backes, C.1    Kuentzer, J.2    Lenhof, H.P.3    Comtesse, N.4    Meese, E.5
  • 14
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (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    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 17
    • 0032749078 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
    • Wright PE, Dyson HJ, (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. Journal of Molecular Biology 293: 321-331.
    • (1999) Journal of Molecular Biology , vol.293 , pp. 321-331
    • Wright, P.E.1    Dyson, H.J.2
  • 19
    • 0036968309 scopus 로고    scopus 로고
    • Loopy proteins appear conserved in evolution
    • Liu J, Tan H, Rost B, (2002) Loopy proteins appear conserved in evolution. Journal of Molecular Biology 322: 53-64.
    • (2002) Journal of Molecular Biology , vol.322 , pp. 53-64
    • Liu, J.1    Tan, H.2    Rost, B.3
  • 20
    • 0036803243 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins
    • Tompa P, (2002) Intrinsically unstructured proteins. Trends in Biochemical Sciences 27: 527-533.
    • (2002) Trends in Biochemical Sciences , vol.27 , pp. 527-533
    • Tompa, P.1
  • 24
    • 24344458137 scopus 로고    scopus 로고
    • Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy
    • Peng H, Long F, Ding C, (2005) Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell 27: 1226-1238.
    • (2005) IEEE Trans Pattern Anal Mach Intell , vol.27 , pp. 1226-1238
    • Peng, H.1    Long, F.2    Ding, C.3
  • 25
    • 84866523368 scopus 로고    scopus 로고
    • Computational Prediction and Analysis of Protein [gamma]-carboxylation Sites Based on a Random Forest Method
    • Zhang N, Li B-Q, Gao S, Ruan J-S, Cai Y-D (2012) Computational Prediction and Analysis of Protein [gamma]-carboxylation Sites Based on a Random Forest Method. Molecular BioSystems.
    • (2012) Molecular BioSystems
    • Zhang, N.1    Li, B.-Q.2    Gao, S.3    Ruan, J.-S.4    Cai, Y.-D.5
  • 26
    • 84862499641 scopus 로고    scopus 로고
    • Prediction of Protein Domain with mRMR Feature Selection and Analysis
    • Li B-Q, Hu L-L, Chen L, Feng K-Y, Cai Y-D, et al. (2012) Prediction of Protein Domain with mRMR Feature Selection and Analysis. PLoS One 7: e39308.
    • (2012) PLoS One , vol.7
    • Li, B.-Q.1    Hu, L.-L.2    Chen, L.3    Feng, K.-Y.4    Cai, Y.-D.5
  • 27
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L, (2001) Random forests. Machine learning 45: 5-32.
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 28
    • 33748902345 scopus 로고    scopus 로고
    • Data Mining: Practical machine learning tools and techniques
    • Witten IH, Frank E (2005) Data Mining: Practical machine learning tools and techniques: Morgan Kaufmann Pub.
    • (2005) Morgan Kaufmann Pub.
    • Witten, I.H.1    Frank, E.2
  • 29
    • 85164392958 scopus 로고
    • A Study of Cross-Validation and Bootstrap for Accuracy Estimation and Model Selection
    • Kohavi R (1995) A Study of Cross-Validation and Bootstrap for Accuracy Estimation and Model Selection. IJCAI. 1137-1145.
    • (1995) IJCAI , pp. 1137-1145
    • Kohavi, R.1
  • 30
    • 84856347308 scopus 로고    scopus 로고
    • Predict and analyze S-nitrosylation modification sites with the mRMR and IFS approaches
    • Li BQ, Hu LL, Niu S, Cai YD, Chou KC, (2012) Predict and analyze S-nitrosylation modification sites with the mRMR and IFS approaches. J Proteomics 75: 1654-1665.
    • (2012) J Proteomics , vol.75 , pp. 1654-1665
    • Li, B.Q.1    Hu, L.L.2    Niu, S.3    Cai, Y.D.4    Chou, K.C.5
  • 31
    • 0032937875 scopus 로고    scopus 로고
    • Carboxy-terminal conversion of profibrillin to fibrillin at a basic site by PACE/furin-like activity required for incorporation in the matrix
    • Raghunath M, Putnam EA, Ritty T, Hamstra D, Park ES, et al. (1999) Carboxy-terminal conversion of profibrillin to fibrillin at a basic site by PACE/furin-like activity required for incorporation in the matrix. J Cell Sci 112 (Pt 7): 1093-1100.
    • (1999) J Cell Sci , vol.112 , Issue.Pt 7 , pp. 1093-1100
    • Raghunath, M.1    Putnam, E.A.2    Ritty, T.3    Hamstra, D.4    Park, E.S.5
  • 32
    • 0038043187 scopus 로고    scopus 로고
    • Paired basic/Furin-like proprotein convertase cleavage of Pro-BMP-1 in the trans-Golgi network
    • Leighton M, Kadler KE, (2003) Paired basic/Furin-like proprotein convertase cleavage of Pro-BMP-1 in the trans-Golgi network. J Biol Chem 278: 18478-18484.
    • (2003) J Biol Chem , vol.278 , pp. 18478-18484
    • Leighton, M.1    Kadler, K.E.2
  • 33
    • 0027337146 scopus 로고
    • Proteolytic processing of the hepatocyte growth factor/scatter factor receptor by furin
    • Komada M, Hatsuzawa K, Shibamoto S, Ito F, Nakayama K, et al. (1993) Proteolytic processing of the hepatocyte growth factor/scatter factor receptor by furin. FEBS Lett 328: 25-29.
    • (1993) FEBS Lett , vol.328 , pp. 25-29
    • Komada, M.1    Hatsuzawa, K.2    Shibamoto, S.3    Ito, F.4    Nakayama, K.5
  • 34
  • 35
    • 17244364283 scopus 로고    scopus 로고
    • Proteases universally recognize beta strands in their active sites
    • Tyndall JD, Nall T, Fairlie DP, (2005) Proteases universally recognize beta strands in their active sites. Chem Rev 105: 973-999.
    • (2005) Chem Rev , vol.105 , pp. 973-999
    • Tyndall, J.D.1    Nall, T.2    Fairlie, D.P.3
  • 36
    • 0034611591 scopus 로고    scopus 로고
    • Conformational selection of inhibitors and substrates by proteolytic enzymes: implications for drug design and polypeptide processing
    • Fairlie DP, Tyndall JD, Reid RC, Wong AK, Abbenante G, et al. (2000) Conformational selection of inhibitors and substrates by proteolytic enzymes: implications for drug design and polypeptide processing. J Med Chem 43: 1271-1281.
    • (2000) J Med Chem , vol.43 , pp. 1271-1281
    • Fairlie, D.P.1    Tyndall, J.D.2    Reid, R.C.3    Wong, A.K.4    Abbenante, G.5
  • 37
    • 34250823439 scopus 로고    scopus 로고
    • Detection of cleavage sites for HIV-1 protease in native proteins
    • You L (2006) Detection of cleavage sites for HIV-1 protease in native proteins. Comput Syst Bioinformatics Conf: 249-256.
    • (2006) Comput Syst Bioinformatics Conf , pp. 249-256
    • You, L.1
  • 38
    • 78149267757 scopus 로고    scopus 로고
    • A redox switch in angiotensinogen modulates angiotensin release
    • Zhou A, Carrell RW, Murphy MP, Wei Z, Yan Y, et al. (2010) A redox switch in angiotensinogen modulates angiotensin release. Nature 468: 108-111.
    • (2010) Nature , vol.468 , pp. 108-111
    • Zhou, A.1    Carrell, R.W.2    Murphy, M.P.3    Wei, Z.4    Yan, Y.5
  • 39
    • 67249086879 scopus 로고    scopus 로고
    • Structural specializations of A2, a force-sensing domain in the ultralarge vascular protein von Willebrand factor
    • Zhang Q, Zhou YF, Zhang CZ, Zhang X, Lu C, et al. (2009) Structural specializations of A2, a force-sensing domain in the ultralarge vascular protein von Willebrand factor. Proc Natl Acad Sci U S A 106: 9226-9231.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 9226-9231
    • Zhang, Q.1    Zhou, Y.F.2    Zhang, C.Z.3    Zhang, X.4    Lu, C.5
  • 41
    • 2442690776 scopus 로고    scopus 로고
    • Proteomic analysis of cleavage events reveals a dynamic two-step mechanism for proteolysis of a key parasite adhesive complex
    • Zhou XW, Blackman MJ, Howell SA, Carruthers VB, (2004) Proteomic analysis of cleavage events reveals a dynamic two-step mechanism for proteolysis of a key parasite adhesive complex. Mol Cell Proteomics 3: 565-576.
    • (2004) Mol Cell Proteomics , vol.3 , pp. 565-576
    • Zhou, X.W.1    Blackman, M.J.2    Howell, S.A.3    Carruthers, V.B.4
  • 42
    • 0842313260 scopus 로고    scopus 로고
    • Prediction of proprotein convertase cleavage sites
    • Duckert P, Brunak S, Blom N, (2004) Prediction of proprotein convertase cleavage sites. Protein Eng Des Sel 17: 107-112.
    • (2004) Protein Eng Des Sel , vol.17 , pp. 107-112
    • Duckert, P.1    Brunak, S.2    Blom, N.3
  • 43
    • 0032935861 scopus 로고    scopus 로고
    • ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites
    • Emanuelsson O, Nielsen H, von Heijne G, (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci 8: 978-984.
    • (1999) Protein Sci , vol.8 , pp. 978-984
    • Emanuelsson, O.1    Nielsen, H.2    von Heijne, G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.