메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

Identification of properties important to protein aggregation using feature selection

Author keywords

Aggregation; Amyloid; Feature selection; Machine learning; Peptide; Prediction

Indexed keywords

AGGREGATION PROPENSITY; AMYLOID; BIOPHARMACEUTICAL INDUSTRY; FEATURE SELECTION ALGORITHM; IDENTIFICATION OF PROPERTIES; PHYSICOCHEMICAL PROPERTY; QUATERNARY STRUCTURE; STATE-OF-THE-ART ALGORITHMS;

EID: 84886130181     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-314     Document Type: Article
Times cited : (31)

References (45)
  • 1
    • 33646106328 scopus 로고    scopus 로고
    • Protein quality in bacterial inclusion bodies
    • 10.1016/j.tibtech.2006.02.007, 16503059
    • Ventura S, Villaverde A. Protein quality in bacterial inclusion bodies. Trends Biotechnol 2006, 24(4):179-185. 10.1016/j.tibtech.2006.02.007, 16503059.
    • (2006) Trends Biotechnol , vol.24 , Issue.4 , pp. 179-185
    • Ventura, S.1    Villaverde, A.2
  • 2
    • 67449132077 scopus 로고    scopus 로고
    • Principles, Approaches, and Challenges for Predicting Protein Aggregation Rates and Shelf Life
    • Weiss WF, Young TM, Roberts CJ. Principles, Approaches, and Challenges for Predicting Protein Aggregation Rates and Shelf Life. J Pharm Sci-Us 2009, 98(4):1246-1277.
    • (2009) J Pharm Sci-Us , vol.98 , Issue.4 , pp. 1246-1277
    • Weiss, W.F.1    Young, T.M.2    Roberts, C.J.3
  • 3
    • 3042584515 scopus 로고    scopus 로고
    • The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates
    • 10.1110/ps.04663504, 2279921, 15169952
    • Tartaglia GG, Cavalli A, Pellarin R, Caflisch A. The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates. Protein Sci 2004, 13(7):1939-1941. 10.1110/ps.04663504, 2279921, 15169952.
    • (2004) Protein Sci , vol.13 , Issue.7 , pp. 1939-1941
    • Tartaglia, G.G.1    Cavalli, A.2    Pellarin, R.3    Caflisch, A.4
  • 4
    • 70349575077 scopus 로고    scopus 로고
    • Functional amyloids signal their arrival
    • 10.1126/scisignal.280pe43, 2838484, 19622831
    • Badtke MP, Hammer ND, Chapman MR. Functional amyloids signal their arrival. Sci Signal 2009, 2(80):pe43. 10.1126/scisignal.280pe43, 2838484, 19622831.
    • (2009) Sci Signal , vol.2 , Issue.80
    • Badtke, M.P.1    Hammer, N.D.2    Chapman, M.R.3
  • 6
    • 28044457195 scopus 로고    scopus 로고
    • The amyloid stretch hypothesis: recruiting proteins toward the dark side
    • 10.1073/pnas.0505905102, 1283810, 16263932
    • Esteras-Chopo A, Serrano L, Lopez De La Paz M. The amyloid stretch hypothesis: recruiting proteins toward the dark side. Proc Natl Acad Sci USA 2005, 102(46):16672-16677. 10.1073/pnas.0505905102, 1283810, 16263932.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.46 , pp. 16672-16677
    • Esteras-Chopo, A.1    Serrano, L.2    Lopez De La Paz, M.3
  • 7
    • 20444440728 scopus 로고    scopus 로고
    • Structure of the cross-beta spine of amyloid-like fibrils
    • 10.1038/nature03680, 1479801, 15944695
    • Nelson R, Sawaya MR, Balbirnie M, Madsen AO, Riekel C, Grothe R, Eisenberg D. Structure of the cross-beta spine of amyloid-like fibrils. Nature 2005, 435(7043):773-778. 10.1038/nature03680, 1479801, 15944695.
    • (2005) Nature , vol.435 , Issue.7043 , pp. 773-778
    • Nelson, R.1    Sawaya, M.R.2    Balbirnie, M.3    Madsen, A.O.4    Riekel, C.5    Grothe, R.6    Eisenberg, D.7
  • 8
    • 33645238380 scopus 로고    scopus 로고
    • The 3D profile method for identifying fibril-forming segments of proteins
    • 10.1073/pnas.0511295103, 1449648, 16537487
    • Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D. The 3D profile method for identifying fibril-forming segments of proteins. Proc Natl Acad Sci USA 2006, 103(11):4074-4078. 10.1073/pnas.0511295103, 1449648, 16537487.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.11 , pp. 4074-4078
    • Thompson, M.J.1    Sievers, S.A.2    Karanicolas, J.3    Ivanova, M.I.4    Baker, D.5    Eisenberg, D.6
  • 9
    • 25844466604 scopus 로고    scopus 로고
    • Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences
    • 10.1110/ps.051471205, 2253302, 16195556
    • Tartaglia GG, Cavalli A, Pellarin R, Caflisch A. Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Protein Sci 2005, 14(10):2723-2734. 10.1110/ps.051471205, 2253302, 16195556.
    • (2005) Protein Sci , vol.14 , Issue.10 , pp. 2723-2734
    • Tartaglia, G.G.1    Cavalli, A.2    Pellarin, R.3    Caflisch, A.4
  • 10
    • 0037044732 scopus 로고    scopus 로고
    • Charge attraction and beta propensity are necessary for amyloid fibril formation from tetrapeptides
    • 10.1074/jbc.M205570200, 12215440
    • Tjernberg L, Hosia W, Bark N, Thyberg J, Johansson J. Charge attraction and beta propensity are necessary for amyloid fibril formation from tetrapeptides. J Biol Chem 2002, 277(45):43243-43246. 10.1074/jbc.M205570200, 12215440.
    • (2002) J Biol Chem , vol.277 , Issue.45 , pp. 43243-43246
    • Tjernberg, L.1    Hosia, W.2    Bark, N.3    Thyberg, J.4    Johansson, J.5
  • 11
    • 79959971250 scopus 로고    scopus 로고
    • Regions which are Responsible for Swapping are also Responsible for Folding and Misfolding
    • 3134983, 21769300
    • Galzitskaya OV. Regions which are Responsible for Swapping are also Responsible for Folding and Misfolding. Open Biochem J 2011, 5:27-36. 3134983, 21769300.
    • (2011) Open Biochem J , vol.5 , pp. 27-36
    • Galzitskaya, O.V.1
  • 12
    • 32344448608 scopus 로고    scopus 로고
    • Protein aggregation and amyloidosis: confusion of the kinds?
    • 10.1016/j.sbi.2006.01.011, 16434184
    • Rousseau F, Schymkowitz J, Serrano L. Protein aggregation and amyloidosis: confusion of the kinds?. Curr Opin Struct Biol 2006, 16(1):118-126. 10.1016/j.sbi.2006.01.011, 16434184.
    • (2006) Curr Opin Struct Biol , vol.16 , Issue.1 , pp. 118-126
    • Rousseau, F.1    Schymkowitz, J.2    Serrano, L.3
  • 13
    • 77953655331 scopus 로고    scopus 로고
    • Potential aggregation prone regions in biotherapeutics A survey of commercial monoclonal antibodies
    • 10.4161/mabs.1.3.8035, 2726584, 20065649
    • Wang XL, Das TK, Singh SK, Kumar S. Potential aggregation prone regions in biotherapeutics A survey of commercial monoclonal antibodies. Mabs 2009, 1(3):254-267. 10.4161/mabs.1.3.8035, 2726584, 20065649.
    • (2009) Mabs , vol.1 , Issue.3 , pp. 254-267
    • Wang, X.L.1    Das, T.K.2    Singh, S.K.3    Kumar, S.4
  • 14
    • 33748525884 scopus 로고    scopus 로고
    • Computational models for the prediction of polypeptide aggregation propensity
    • 10.1016/j.cbpa.2006.07.009, 16880001
    • Caflisch A. Computational models for the prediction of polypeptide aggregation propensity. Curr Opin Chem Biol 2006, 10(5):437-444. 10.1016/j.cbpa.2006.07.009, 16880001.
    • (2006) Curr Opin Chem Biol , vol.10 , Issue.5 , pp. 437-444
    • Caflisch, A.1
  • 15
    • 5044235541 scopus 로고    scopus 로고
    • Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
    • 10.1038/nbt1012, 15361882
    • Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat Biotechnol 2004, 22(10):1302-1306. 10.1038/nbt1012, 15361882.
    • (2004) Nat Biotechnol , vol.22 , Issue.10 , pp. 1302-1306
    • Fernandez-Escamilla, A.M.1    Rousseau, F.2    Schymkowitz, J.3    Serrano, L.4
  • 16
    • 34547681771 scopus 로고    scopus 로고
    • Expected packing density allows prediction of both amyloidogenic and disordered regions in protein chains
    • Galzitskaya OV, Garbuzynskiy SO, Lobanov MY. Expected packing density allows prediction of both amyloidogenic and disordered regions in protein chains. J Phys Condens Matter 2007, 19(28):1-15.
    • (2007) J Phys Condens Matter , vol.19 , Issue.28 , pp. 1-15
    • Galzitskaya, O.V.1    Garbuzynskiy, S.O.2    Lobanov, M.Y.3
  • 17
  • 18
    • 20444403757 scopus 로고    scopus 로고
    • Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases
    • 10.1016/j.jmb.2005.04.016, 15925383
    • Pawar AP, DuBay KF, Zurdo J, Chiti F, Vendruscolo M, Dobson CM. Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases. Journal of molecular biology 2005, 350(2):379-392. 10.1016/j.jmb.2005.04.016, 15925383.
    • (2005) Journal of molecular biology , vol.350 , Issue.2 , pp. 379-392
    • Pawar, A.P.1    DuBay, K.F.2    Zurdo, J.3    Chiti, F.4    Vendruscolo, M.5    Dobson, C.M.6
  • 19
    • 33947517558 scopus 로고    scopus 로고
    • AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides
    • Conchillo-Sole O, de Groot NS, Aviles FX, Vendrell J, Daura X, Ventura S. AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides. BMC Bioinforma 2007, 8(65):1-17.
    • (2007) BMC Bioinforma , vol.8 , Issue.65 , pp. 1-17
    • Conchillo-Sole, O.1    de Groot, N.S.2    Aviles, F.X.3    Vendrell, J.4    Daura, X.5    Ventura, S.6
  • 20
    • 60849089613 scopus 로고    scopus 로고
    • Prediction of amyloid fibril-forming segments based on a support vector machine
    • Tian J, Wu N, Guo J, Fan Y. Prediction of amyloid fibril-forming segments based on a support vector machine. BMC Bioinforma 2009, 10(Suppl 1):S45.
    • (2009) BMC Bioinforma , vol.10 , Issue.SUPPL 1
    • Tian, J.1    Wu, N.2    Guo, J.3    Fan, Y.4
  • 21
    • 0042467550 scopus 로고    scopus 로고
    • Rationalization of the effects of mutations on peptide and protein aggregation rates
    • 10.1038/nature01891, 12917692
    • Chiti F, Stefani M, Taddei N, Ramponi G, Dobson CM. Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature 2003, 424(6950):805-808. 10.1038/nature01891, 12917692.
    • (2003) Nature , vol.424 , Issue.6950 , pp. 805-808
    • Chiti, F.1    Stefani, M.2    Taddei, N.3    Ramponi, G.4    Dobson, C.M.5
  • 22
    • 3242785264 scopus 로고    scopus 로고
    • Prediction of the absolute aggregation rates of amyloidogenic polypeptide chains
    • 10.1016/j.jmb.2004.06.043, 15302561
    • Dubay KF, Pawar AP, Chiti F, Zurdo J, Dobson CM, Vendruscolo M. Prediction of the absolute aggregation rates of amyloidogenic polypeptide chains. Journal of molecular biology 2004, 341(5):1317-1326. 10.1016/j.jmb.2004.06.043, 15302561.
    • (2004) Journal of molecular biology , vol.341 , Issue.5 , pp. 1317-1326
    • Dubay, K.F.1    Pawar, A.P.2    Chiti, F.3    Zurdo, J.4    Dobson, C.M.5    Vendruscolo, M.6
  • 23
    • 33845990277 scopus 로고    scopus 로고
    • Prediction of amyloidogenic and disordered regions in protein chains
    • Galzitskaya OV, Garbuzynskiy SO, Lobanov MY. Prediction of amyloidogenic and disordered regions in protein chains. PLoS Comput Biol 2006, 2(12):1639-1648.
    • (2006) PLoS Comput Biol , vol.2 , Issue.12 , pp. 1639-1648
    • Galzitskaya, O.V.1    Garbuzynskiy, S.O.2    Lobanov, M.Y.3
  • 24
    • 0032594959 scopus 로고    scopus 로고
    • An overview of statistical learning theory
    • Vapnik VN. An overview of statistical learning theory. Ieee T Neural Networ 1999, 10(5):988-999.
    • (1999) Ieee T Neural Networ , vol.10 , Issue.5 , pp. 988-999
    • Vapnik, V.N.1
  • 25
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. Random forests. Mach Learn 2001, 45(1):5-32.
    • (2001) Mach Learn , vol.45 , Issue.1 , pp. 5-32
    • Breiman, L.1
  • 26
    • 0036150827 scopus 로고    scopus 로고
    • Alzheimer's disease - do tauists and baptists finally shake hands?
    • 10.1016/S0166-2236(00)02031-2, 11801334
    • Mudher A, Lovestone S. Alzheimer's disease - do tauists and baptists finally shake hands?. Trends Neurosci 2002, 25(1):22-26. 10.1016/S0166-2236(00)02031-2, 11801334.
    • (2002) Trends Neurosci , vol.25 , Issue.1 , pp. 22-26
    • Mudher, A.1    Lovestone, S.2
  • 28
    • 0025323708 scopus 로고
    • The distribution of physical, chemical and conformational properties in signal and nascent peptides
    • 1131643, 2390062
    • Prabhakaran M. The distribution of physical, chemical and conformational properties in signal and nascent peptides. Biochem J 1990, 269(3):691-696. 1131643, 2390062.
    • (1990) Biochem J , vol.269 , Issue.3 , pp. 691-696
    • Prabhakaran, M.1
  • 29
    • 0033044637 scopus 로고    scopus 로고
    • Machine learning approaches for the prediction of signal peptides and other protein sorting signals
    • 10.1093/protein/12.1.3, 10065704
    • Nielsen H, Brunak S, von Heijne G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein engineering 1999, 12(1):3-9. 10.1093/protein/12.1.3, 10065704.
    • (1999) Protein engineering , vol.12 , Issue.1 , pp. 3-9
    • Nielsen, H.1    Brunak, S.2    von Heijne, G.3
  • 30
    • 0030614959 scopus 로고    scopus 로고
    • Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
    • Nielsen H, Engelbrecht J, Brunak S, VonHeijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein engineering 1997, 10(1):1-6.
    • (1997) Protein engineering , vol.10 , Issue.1 , pp. 1-6
    • Nielsen, H.1    Engelbrecht, J.2    Brunak, S.3    VonHeijne, G.4
  • 31
    • 77958487260 scopus 로고    scopus 로고
    • Cellular strategies for controlling protein aggregation
    • Tyedmers J, Mogk A, Bukau B. Cellular strategies for controlling protein aggregation. Nat Rev Mol Cell Bio 2010, 11(11):777-788.
    • (2010) Nat Rev Mol Cell Bio , vol.11 , Issue.11 , pp. 777-788
    • Tyedmers, J.1    Mogk, A.2    Bukau, B.3
  • 32
    • 0031603460 scopus 로고    scopus 로고
    • Prediction of signal peptides and signal anchors by a hidden Markov model
    • Nielsen H, Krogh A. Prediction of signal peptides and signal anchors by a hidden Markov model. Proc Int Conf Intell Syst Mol Biol 1998, 6:122-130.
    • (1998) Proc Int Conf Intell Syst Mol Biol , vol.6 , pp. 122-130
    • Nielsen, H.1    Krogh, A.2
  • 34
    • 0035470889 scopus 로고    scopus 로고
    • Greedy function approximation: a gradient boosting machine
    • Friedman JH. Greedy function approximation: a gradient boosting machine. Ann Stat 2001, 29(5):1189-1232.
    • (2001) Ann Stat , vol.29 , Issue.5 , pp. 1189-1232
    • Friedman, J.H.1
  • 36
    • 11144273669 scopus 로고
    • The Perceptron - a Probabilistic model for information-storage and organization in the brain
    • Rosenblatt F. The Perceptron - a Probabilistic model for information-storage and organization in the brain. Psychol Rev 1958, 65(6):386-408.
    • (1958) Psychol Rev , vol.65 , Issue.6 , pp. 386-408
    • Rosenblatt, F.1
  • 37
    • 28544443804 scopus 로고    scopus 로고
    • A beginner's guide to partial least squares analysis
    • Haenlein M, Kaplan AM. A beginner's guide to partial least squares analysis. Underst Stat 2004, 3(4):283-297.
    • (2004) Underst Stat , vol.3 , Issue.4 , pp. 283-297
    • Haenlein, M.1    Kaplan, A.M.2
  • 38
    • 84926662675 scopus 로고
    • Nearest neighbor pattern classification
    • Cover TM, Hart PE. Nearest neighbor pattern classification. Ieee T Inform Theory 1967, 13(1):21-27.
    • (1967) Ieee T Inform Theory , vol.13 , Issue.1 , pp. 21-27
    • Cover, T.M.1    Hart, P.E.2
  • 39
  • 40
    • 0031211090 scopus 로고    scopus 로고
    • A decision-theoretic generalization of on-line learning and an application to boosting
    • Freund Y, Schapire RE. A decision-theoretic generalization of on-line learning and an application to boosting. J Comput Syst Sci 1997, 55(1):119-139.
    • (1997) J Comput Syst Sci , vol.55 , Issue.1 , pp. 119-139
    • Freund, Y.1    Schapire, R.E.2
  • 41
    • 56249113343 scopus 로고    scopus 로고
    • Building Predictive Models in R Using the caret Package
    • Kuhn M. Building Predictive Models in R Using the caret Package. J Stat Softw 2008, 28(5):1-26.
    • (2008) J Stat Softw , vol.28 , Issue.5 , pp. 1-26
    • Kuhn, M.1
  • 42
    • 0036161259 scopus 로고    scopus 로고
    • Gene selection for cancer classification using support vector machines
    • Guyon S, Weston J, Barnhill S. Gene selection for cancer classification using support vector machines. Mach Learn 2002, 46:389-422.
    • (2002) Mach Learn , vol.46 , pp. 389-422
    • Guyon, S.1    Weston, J.2    Barnhill, S.3
  • 43
    • 35348970485 scopus 로고    scopus 로고
    • A web-based tool and R package for gene selection and classification using random forest
    • Diaz-Uriarte R, Gene SF, Var Sel RF. A web-based tool and R package for gene selection and classification using random forest. BMC Bioinforma 2007, 8:328.
    • (2007) BMC Bioinforma , vol.8 , pp. 328
    • Diaz-Uriarte, R.1    Gene, S.F.2    Var Sel, R.F.3
  • 45
    • 0033613188 scopus 로고    scopus 로고
    • De novo amyloid proteins from designed combinatorial libraries
    • 10.1073/pnas.96.20.11211, 18013, 10500156
    • West MW, Wang WX, Patterson J, Mancias JD, Beasley JR, Hecht MH. De novo amyloid proteins from designed combinatorial libraries. Proc Natl Acad Sci USA 1999, 96(20):11211-11216. 10.1073/pnas.96.20.11211, 18013, 10500156.
    • (1999) Proc Natl Acad Sci USA , vol.96 , Issue.20 , pp. 11211-11216
    • West, M.W.1    Wang, W.X.2    Patterson, J.3    Mancias, J.D.4    Beasley, J.R.5    Hecht, M.H.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.