메뉴 건너뛰기




Volumn 11, Issue , 2010, Pages

Pripper: Prediction of caspase cleavage sites from whole proteomes

Author keywords

[No Author keywords available]

Indexed keywords

ARBITRARY NUMBER; CLEAVAGE PRODUCTS; INDIVIDUAL PROTEINS; PATTERN RECOGNITION CLASSIFIERS; PREDICTION MODEL; PROGRAMMED CELL DEATHS; PROTEIN SEQUENCES; TANDEM MASS SPECTROMETRY;

EID: 77954272392     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-320     Document Type: Article
Times cited : (36)

References (23)
  • 3
    • 33947426526 scopus 로고    scopus 로고
    • The CASBAH: a searchable database of caspase substrates
    • 10.1038/sj.cdd.4402103, 17273173
    • Lüthi AU, Martin SJ. The CASBAH: a searchable database of caspase substrates. Cell Death Differ 2007, 14:641-650. 10.1038/sj.cdd.4402103, 17273173.
    • (2007) Cell Death Differ , vol.14 , pp. 641-650
    • Lüthi, A.U.1    Martin, S.J.2
  • 5
    • 0030849093 scopus 로고    scopus 로고
    • A combinatorial approach defines specificities of members of the caspase family and granzyme B. Functional relationships established for key mediators of apoptosis
    • 10.1074/jbc.272.29.17907, 9218414
    • Thornberry NA, Rano TA, Peterson EP, Rasper DM, Timkey T, Garcia-Calvo M, Houtzager VM, Nordstrom PA, Roy S, Vaillancourt JP, et al. A combinatorial approach defines specificities of members of the caspase family and granzyme B. Functional relationships established for key mediators of apoptosis. J Biol Chem 1997, 272:17907-17911. 10.1074/jbc.272.29.17907, 9218414.
    • (1997) J Biol Chem , vol.272 , pp. 17907-17911
    • Thornberry, N.A.1    Rano, T.A.2    Peterson, E.P.3    Rasper, D.M.4    Timkey, T.5    Garcia-Calvo, M.6    Houtzager, V.M.7    Nordstrom, P.A.8    Roy, S.9    Vaillancourt, J.P.10
  • 6
    • 52649141086 scopus 로고    scopus 로고
    • Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini
    • 10.1016/j.cell.2008.08.012, 2566540, 18722006
    • Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA. Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell 2008, 134:866-876. 10.1016/j.cell.2008.08.012, 2566540, 18722006.
    • (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    Wells, J.A.6
  • 7
    • 0038824700 scopus 로고    scopus 로고
    • Toward computer-based cleavage site prediction of cysteine endopeptidases
    • 10.1515/BC.2003.101, 12887057
    • Lohmüller T, Wenzler D, Hagemann S, Kiess W, Peters C, Dandekar T, Reinheckel T. Toward computer-based cleavage site prediction of cysteine endopeptidases. Biol Chem 2003, 384:899-909. 10.1515/BC.2003.101, 12887057.
    • (2003) Biol Chem , vol.384 , pp. 899-909
    • Lohmüller, T.1    Wenzler, D.2    Hagemann, S.3    Kiess, W.4    Peters, C.5    Dandekar, T.6    Reinheckel, T.7
  • 8
    • 29144473665 scopus 로고    scopus 로고
    • CaSPredictor: a new computer-based tool for caspase substrate prediction
    • 10.1093/bioinformatics/bti1034, 15961454
    • Garay-Malpartida HM, Occhiucci JM, Alves J, Belizario JE. CaSPredictor: a new computer-based tool for caspase substrate prediction. Bioinformatics 2005, 21:i169-i176. 10.1093/bioinformatics/bti1034, 15961454.
    • (2005) Bioinformatics , vol.21
    • Garay-Malpartida, H.M.1    Occhiucci, J.M.2    Alves, J.3    Belizario, J.E.4
  • 9
    • 23144444029 scopus 로고    scopus 로고
    • GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences
    • 10.1093/nar/gki433, 1160194, 15980455
    • Backes C, Kuentzer J, Lenhof HP, Comtesse N, Meese E. GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences. Nucleic Acids Res 2005, 33:W208-W213. 10.1093/nar/gki433, 1160194, 15980455.
    • (2005) Nucleic Acids Res , vol.33
    • Backes, C.1    Kuentzer, J.2    Lenhof, H.P.3    Comtesse, N.4    Meese, E.5
  • 10
    • 84871967410 scopus 로고    scopus 로고
    • SVM-based prediction of caspase substrate cleavage sites
    • 10.1186/1471-2105-7-S5-S14, 1764470, 17254298
    • Wee L, Tan T, Ranganathan S. SVM-based prediction of caspase substrate cleavage sites. BMC Bioinformatics 2006, 7:S14. 10.1186/1471-2105-7-S5-S14, 1764470, 17254298.
    • (2006) BMC Bioinformatics , vol.7
    • Wee, L.1    Tan, T.2    Ranganathan, S.3
  • 11
    • 18744369642 scopus 로고    scopus 로고
    • Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks
    • 10.1093/bioinformatics/bti281, 15671118
    • Yang ZR. Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks. Bioinformatics 2005, 21:1831-1837. 10.1093/bioinformatics/bti281, 15671118.
    • (2005) Bioinformatics , vol.21 , pp. 1831-1837
    • Yang, Z.R.1
  • 12
    • 71549169257 scopus 로고    scopus 로고
    • A multi-factor model for caspase degradome prediction
    • 10.1186/1471-2164-10-S3-S6, 2788393, 19958504
    • Wee LJ, Tong JC, Tan TW, Ranganathan S. A multi-factor model for caspase degradome prediction. BMC Genomics 2009, 10(Suppl 3):S6. 10.1186/1471-2164-10-S3-S6, 2788393, 19958504.
    • (2009) BMC Genomics , vol.10 , Issue.SUPPL 3
    • Wee, L.J.1    Tong, J.C.2    Tan, T.W.3    Ranganathan, S.4
  • 13
    • 34249753618 scopus 로고
    • Support-Vector networks
    • Cortes C, Vapnik V. Support-Vector networks. Mach Learn 1995, 20:273-297.
    • (1995) Mach Learn , vol.20 , pp. 273-297
    • Cortes, C.1    Vapnik, V.2
  • 14
    • 0035478854 scopus 로고    scopus 로고
    • Random Forests
    • Breiman L. Random Forests. Mach Learn 2001, 45:5-32.
    • (2001) Mach Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 16
    • 49549113643 scopus 로고    scopus 로고
    • Global mapping of the topography and magnitude of proteolytic events in apoptosis
    • 10.1016/j.cell.2008.06.038, 2597167, 18724940
    • Dix MM, Simon GM, Cravatt BF. Global mapping of the topography and magnitude of proteolytic events in apoptosis. Cell 2008, 134:679-691. 10.1016/j.cell.2008.06.038, 2597167, 18724940.
    • (2008) Cell , vol.134 , pp. 679-691
    • Dix, M.M.1    Simon, G.M.2    Cravatt, B.F.3
  • 17
    • 27144489164 scopus 로고    scopus 로고
    • A Tutorial on Support Vector Machines for Pattern Recognition
    • Burges CJC. A Tutorial on Support Vector Machines for Pattern Recognition. Dat Min Knowl Disc 1998, 2:121-167.
    • (1998) Dat Min Knowl Disc , vol.2 , pp. 121-167
    • Burges, C.J.C.1
  • 18
    • 0003710380 scopus 로고    scopus 로고
    • LIBSVM: a library for support vector machines
    • Chang C-C, Lin C-J. LIBSVM: a library for support vector machines. 2001, , http://www.csie.ntu.edu.tw/~cjlin/libsvm
    • (2001)
    • Chang, C.-.C.1    Lin, C.-.J.2
  • 20
    • 77949829296 scopus 로고    scopus 로고
    • Cytosolic RNA recognition pathway activates 14-3-3 protein mediated signaling and caspase-dependent disruption of cytokeratin network in human keratinocytes
    • 10.1021/pr901040u, 20070120
    • Öhman T, Lietzen N, Välimaki E, Melchjorsen J, Matikainen S, Nyman TA. Cytosolic RNA recognition pathway activates 14-3-3 protein mediated signaling and caspase-dependent disruption of cytokeratin network in human keratinocytes. J Proteome Res 2010, 9:1549-1564. 10.1021/pr901040u, 20070120.
    • (2010) J Proteome Res , vol.9 , pp. 1549-1564
    • Öhman, T.1    Lietzen, N.2    Välimaki, E.3    Melchjorsen, J.4    Matikainen, S.5    Nyman, T.A.6
  • 21
    • 58049220320 scopus 로고    scopus 로고
    • Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature
    • 10.1093/bioinformatics/btn583, 2638931, 19008251
    • Wu J, Liu H, Duan X, Ding Y, Wu H, Bai Y, Sun X. Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature. Bioinformatics 2009, 25:30-35. 10.1093/bioinformatics/btn583, 2638931, 19008251.
    • (2009) Bioinformatics , vol.25 , pp. 30-35
    • Wu, J.1    Liu, H.2    Duan, X.3    Ding, Y.4    Wu, H.5    Bai, Y.6    Sun, X.7
  • 22
    • 33646023117 scopus 로고    scopus 로고
    • 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
  • 23
    • 0036803243 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins
    • 10.1016/S0968-0004(02)02169-2, 12368089
    • Tompa P. Intrinsically unstructured proteins. Trends in Biochemical Sciences 2002, 27:527-533. 10.1016/S0968-0004(02)02169-2, 12368089.
    • (2002) Trends in Biochemical Sciences , vol.27 , pp. 527-533
    • Tompa, P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.