메뉴 건너뛰기




Volumn 14, Issue , 2013, Pages

Learning a peptide-protein binding affinity predictor with kernel ridge regression

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMIC PROGRAMMING ALGORITHM; KERNEL RIDGE REGRESSIONS; LINEAR-TIME ALGORITHMS; MAJOR HISTOCOMPATIBILITY COMPLEX CLASS; PHYSICO-CHEMICAL PROPERTIES OF AMINO ACIDS; PROTEIN-PROTEIN INTERACTIONS; QUANTITATIVE STRUCTURES; STATE-OF-THE-ART METHODS;

EID: 84877639844     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-82     Document Type: Article
Times cited : (35)

References (36)
  • 1
    • 0037061646 scopus 로고    scopus 로고
    • Inhibition of protein-protein association by small molecules: approaches and progress
    • 10.1021/jm010468s, 11931608
    • Toogood PL. Inhibition of protein-protein association by small molecules: approaches and progress. J Med Chem 2002, 45(8):1543-1558. 10.1021/jm010468s, 11931608.
    • (2002) J Med Chem , vol.45 , Issue.8 , pp. 1543-1558
    • Toogood, P.L.1
  • 2
    • 27944493925 scopus 로고    scopus 로고
    • Scale-free networks in cell biology
    • 10.1242/jcs.02714, 16254242
    • Albert R. Scale-free networks in cell biology. J Cell Sci 2005, 118(Pt 21):4947-4957. 10.1242/jcs.02714, 16254242.
    • (2005) J Cell Sci , vol.118 , Issue.PART 21 , pp. 4947-4957
    • Albert, R.1
  • 3
    • 37249004920 scopus 로고    scopus 로고
    • Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
    • 10.1038/nature06526, 18075579
    • Wells J, McClendon CL. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007, 450(7172):1001-1009. 10.1038/nature06526, 18075579.
    • (2007) Nature , vol.450 , Issue.7172 , pp. 1001-1009
    • Wells, J.1    McClendon, C.L.2
  • 4
    • 44949154279 scopus 로고    scopus 로고
    • Small molecular weight protein-protein interaction antagonists-an insurmountable challenge?
    • 10.1016/j.cbpa.2008.04.603, 18501203
    • Dömling A. Small molecular weight protein-protein interaction antagonists-an insurmountable challenge?. Curr Opin Chem Biol 2008, 12(3):281-291. 10.1016/j.cbpa.2008.04.603, 18501203.
    • (2008) Curr Opin Chem Biol , vol.12 , Issue.3 , pp. 281-291
    • Dömling, A.1
  • 5
    • 33644872086 scopus 로고    scopus 로고
    • Privileged structures as leads in medicinal chemistry
    • Costantino L, Barlocco D. Privileged structures as leads in medicinal chemistry. Curr Med Chem 2006, 65-85. [http://www.ingentaconnect.com/content/ben/cmc/2006/00000013/00000001/art00007].
    • (2006) Curr Med Chem , pp. 65-85
    • Costantino, L.1    Barlocco, D.2
  • 6
    • 33846060813 scopus 로고    scopus 로고
    • Modulation of protein-protein interactions by stabilizing/mimicking protein secondary structure elements
    • 10.2174/156802607779318325, 17266595
    • Perez-De-Vega JM, Martin-Martinez M, Gonzalez-Muniz R. Modulation of protein-protein interactions by stabilizing/mimicking protein secondary structure elements. Curr Top Med Chem 2007, 7:33-62. [http://www.ingentaconnect.com/content/ben/ctmc/2007/00000007/00000001/art00006], 10.2174/156802607779318325, 17266595.
    • (2007) Curr Top Med Chem , vol.7 , pp. 33-62
    • Perez-De-Vega, J.M.1    Martin-Martinez, M.2    Gonzalez-Muniz, R.3
  • 7
    • 52749098733 scopus 로고    scopus 로고
    • Virtual screening of GPCRs: an in silico chemogenomics approach
    • 10.1186/1471-2105-9-363, 2553090, 18775075
    • Jacob L, Hoffmann B, Stoven V, Vert JP. Virtual screening of GPCRs: an in silico chemogenomics approach. BMC Bioinformatics 2008, 9:363. 10.1186/1471-2105-9-363, 2553090, 18775075.
    • (2008) BMC Bioinformatics , vol.9 , pp. 363
    • Jacob, L.1    Hoffmann, B.2    Stoven, V.3    Vert, J.P.4
  • 8
    • 38849139819 scopus 로고    scopus 로고
    • Efficient peptide-MHC-I binding prediction for alleles with few known binders
    • 10.1093/bioinformatics/btm611, 18083718
    • Jacob L, Vert JP. Efficient peptide-MHC-I binding prediction for alleles with few known binders. Bioinformatics 2008, 24(3):358-366. 10.1093/bioinformatics/btm611, 18083718.
    • (2008) Bioinformatics , vol.24 , Issue.3 , pp. 358-366
    • Jacob, L.1    Vert, J.P.2
  • 9
    • 84866446560 scopus 로고    scopus 로고
    • Drug target prediction using adverse event report systems: a pharmacogenomic approach
    • 10.1093/bioinformatics/bts413, 3436840, 22962489
    • Takarabe M, Kotera M, Nishimura Y, Goto S, Yamanishi Y. Drug target prediction using adverse event report systems: a pharmacogenomic approach. Bioinformatics 2012, 28(18):i611-i618. 10.1093/bioinformatics/bts413, 3436840, 22962489.
    • (2012) Bioinformatics , vol.28 , Issue.18
    • Takarabe, M.1    Kotera, M.2    Nishimura, Y.3    Goto, S.4    Yamanishi, Y.5
  • 11
    • 84877669631 scopus 로고    scopus 로고
    • Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools
    • Zhang L, Udaka K, Mamitsuka H, Zhu S. Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools. Brief Bioinform 2011,
    • (2011) Brief Bioinform
    • Zhang, L.1    Udaka, K.2    Mamitsuka, H.3    Zhu, S.4
  • 12
    • 77956922389 scopus 로고    scopus 로고
    • MultiRTA: A simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes
    • 10.1186/1471-2105-11-482, 2957400, 20868497
    • Bordner AJ, Mittelmann HD. MultiRTA: A simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes. BMC Bioinformatics 2010, 11:482. [http://dblp.uni-trier.de/db/journals/bmcbi/bmcbi11.html#BordnerM10a], 10.1186/1471-2105-11-482, 2957400, 20868497.
    • (2010) BMC Bioinformatics , vol.11 , pp. 482
    • Bordner, A.J.1    Mittelmann, H.D.2
  • 13
    • 78149354807 scopus 로고    scopus 로고
    • NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure
    • 10.1186/1745-7580-6-9, 2994798, 21073747
    • Nielsen M, Justesen S, Lund O, Lundegaard C, Buus S. NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure. Immunome Res 2010, 6:9. [http://www.immunome-research.com/content/6/1/9], 10.1186/1745-7580-6-9, 2994798, 21073747.
    • (2010) Immunome Res , vol.6 , pp. 9
    • Nielsen, M.1    Justesen, S.2    Lund, O.3    Lundegaard, C.4    Buus, S.5
  • 15
    • 13244260800 scopus 로고    scopus 로고
    • Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites
    • 10.1186/1471-2105-14-82, 535353, 15511290
    • Meinicke P, Tech M, Morgenstern B, Merkl R. Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites. BMC Bioinformatics 2004, 5:169+. 10.1186/1471-2105-14-82, 535353, 15511290.
    • (2004) BMC Bioinformatics , vol.5
    • Meinicke, P.1    Tech, M.2    Morgenstern, B.3    Merkl, R.4
  • 16
    • 29144515642 scopus 로고    scopus 로고
    • Accurate splice site detection for caenorhabditis elegans
    • : MIT Press, B , Vert JP
    • Rätsch G, Sonnenburg S. Accurate splice site detection for caenorhabditis elegans. Kernel Methods Comput Biol 2004, 277-298. : MIT Press, B , Vert JP, [http://www.fml.tuebingen.mpg.de/raetsch/projects/MITBookSplice/files/RaeSon04.pdf].
    • (2004) Kernel Methods Comput Biol , pp. 277-298
    • Rätsch, G.1    Sonnenburg, S.2
  • 17
    • 4043137356 scopus 로고    scopus 로고
    • A tutorial on support vector regression
    • Smola AJ, Schölkopf B. A tutorial on support vector regression. Stat Comput 2004, 14:199-222..
    • (2004) Stat Comput , vol.14
    • Smola, A.J.1    Schölkopf, B.2
  • 18
    • 76449103795 scopus 로고    scopus 로고
    • Gaussian process: an alternative approach for QSAM modeling of peptides
    • 10.1007/s00726-008-0228-1, 19123053
    • Zhou P, Chen X, Wu Y, Shang Z. Gaussian process: an alternative approach for QSAM modeling of peptides. Amino Acids 2010, 38:199-212. 10.1007/s00726-008-0228-1, 19123053.
    • (2010) Amino Acids , vol.38 , pp. 199-212
    • Zhou, P.1    Chen, X.2    Wu, Y.3    Shang, Z.4
  • 20
    • 34548128437 scopus 로고    scopus 로고
    • Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data
    • 10.1093/bioinformatics/btm266, 17510168
    • Nagamine N, Sakakibara Y. Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data. Bioinformatics 2007, 23(15):2004-2012. 10.1093/bioinformatics/btm266, 17510168.
    • (2007) Bioinformatics , vol.23 , Issue.15 , pp. 2004-2012
    • Nagamine, N.1    Sakakibara, Y.2
  • 21
    • 38349114038 scopus 로고    scopus 로고
    • Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor
    • 10.1093/bioinformatics/btm580, 18037612
    • Faulon JL, Misra M, Martin S, Sale K, Sapra R. Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor. Bioinformatics 2008, 24(2):225-233. 10.1093/bioinformatics/btm580, 18037612.
    • (2008) Bioinformatics , vol.24 , Issue.2 , pp. 225-233
    • Faulon, J.L.1    Misra, M.2    Martin, S.3    Sale, K.4    Sapra, R.5
  • 22
    • 4444273377 scopus 로고    scopus 로고
    • Protein homology detection using string alignment kernels
    • 10.1093/bioinformatics/bth141, 14988126
    • Saigo H, Vert JP, Ueda N, Akutsu T. Protein homology detection using string alignment kernels. Bioinformatics 2004, 20(11):1682-1689. [http://bioinformatics.oxfordjournals.org/content/20/11/1682.abstract], 10.1093/bioinformatics/bth141, 14988126.
    • (2004) Bioinformatics , vol.20 , Issue.11 , pp. 1682-1689
    • Saigo, H.1    Vert, J.P.2    Ueda, N.3    Akutsu, T.4
  • 23
    • 78049461176 scopus 로고    scopus 로고
    • Exploiting physico-chemical properties in string kernels
    • 10.1186/1471-2105-11-S8-S7, 3040533, 21210986
    • Toussaint N, Widmer C, Kohlbacher O, Rätsch G. Exploiting physico-chemical properties in string kernels. BMC Bioinformatics 2010, 11(Suppl 8):S7. 10.1186/1471-2105-11-S8-S7, 3040533, 21210986.
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL. 8
    • Toussaint, N.1    Widmer, C.2    Kohlbacher, O.3    Rätsch, G.4
  • 24
    • 1542714925 scopus 로고    scopus 로고
    • Mismatch string kernels for discriminative protein classification
    • 10.1093/bioinformatics/btg431, 14990442
    • Leslie CS, Eskin E, Cohen A, Weston J, Noble WS. Mismatch string kernels for discriminative protein classification. Bioinformatics 2004, 20(4):467-476. 10.1093/bioinformatics/btg431, 14990442.
    • (2004) Bioinformatics , vol.20 , Issue.4 , pp. 467-476
    • Leslie, C.S.1    Eskin, E.2    Cohen, A.3    Weston, J.4    Noble, W.S.5
  • 26
    • 77950423796 scopus 로고    scopus 로고
    • A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction
    • 10.1186/1471-2105-11-99, 2838872, 20175916
    • Hoffmann B, Zaslavskiy M, Vert JP, Stoven V. A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction. BMC Bioinformatics 2010, 11:99+. 10.1186/1471-2105-11-99, 2838872, 20175916.
    • (2010) BMC Bioinformatics , vol.11
    • Hoffmann, B.1    Zaslavskiy, M.2    Vert, J.P.3    Stoven, V.4
  • 27
    • 38349064624 scopus 로고    scopus 로고
    • A structural alignment kernel for protein structures A structural alignment kernel for protein structures
    • Qiu J, Hue M, Ben-Hur A, Vert JPP, Noble WSS. A structural alignment kernel for protein structures A structural alignment kernel for protein structures. Bioinformatics 2007,
    • (2007) Bioinformatics
    • Qiu, J.1    Hue, M.2    Ben-Hur, A.3    Vert, J.P.P.4    Noble, W.S.S.5
  • 28
    • 0036839162 scopus 로고    scopus 로고
    • MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison
    • 10.1110/ps.0215902, 2373724, 12381844
    • Ortiz AR, Strauss CE, Olmea O. MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison. Protein Sci 2002, 11(11):2606-2621. 10.1110/ps.0215902, 2373724, 12381844.
    • (2002) Protein Sci , vol.11 , Issue.11 , pp. 2606-2621
    • Ortiz, A.R.1    Strauss, C.E.2    Olmea, O.3
  • 29
    • 77952305592 scopus 로고    scopus 로고
    • Large-scale prediction of protein-protein interactions from structures
    • 10.1186/1471-2105-11-144, 2845582, 20298601
    • Hue M, Riffle M, Vert JP, Noble W. Large-scale prediction of protein-protein interactions from structures. BMC Bioinformatics 2010, 11:144+. 10.1186/1471-2105-11-144, 2845582, 20298601.
    • (2010) BMC Bioinformatics , vol.11
    • Hue, M.1    Riffle, M.2    Vert, J.P.3    Noble, W.4
  • 30
    • 0023890867 scopus 로고
    • Measuring the accuracy of diagnostic systems
    • 10.1126/science.3287615, 3287615
    • Swets J. Measuring the accuracy of diagnostic systems. Science 1988, 240(4857):1285-1293. [http://www.sciencemag.org/content/240/4857/1285.abstract], 10.1126/science.3287615, 3287615.
    • (1988) Science , vol.240 , Issue.4857 , pp. 1285-1293
    • Swets, J.1
  • 31
    • 75549088586 scopus 로고    scopus 로고
    • PepX: a structural database of non-redundant protein-peptide complexes
    • Database issue, 10.1093/nar/gkp893, 2808939, 19880386
    • Vanhee P, Reumers J, Stricher F, Baeten L, Serrano L, Schymkowitz J, Rousseau F. PepX: a structural database of non-redundant protein-peptide complexes. Nucleic Acids Res 2010, 38(Database issue):D545-D551. 10.1093/nar/gkp893, 2808939, 19880386.
    • (2010) Nucleic Acids Res , vol.38
    • Vanhee, P.1    Reumers, J.2    Stricher, F.3    Baeten, L.4    Serrano, L.5    Schymkowitz, J.6    Rousseau, F.7
  • 33
    • 77649176463 scopus 로고    scopus 로고
    • Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model
    • 10.1186/1471-2105-11-41, 2828437, 20089173
    • Bordner AJ, Mittelmann HD. Prediction of the binding affinities of peptides to class II MHC using a regularized thermodynamic model. BMC Bioinformatics 2010, 11:41. [http://www.biomedcentral.com/1471-2105/11/41], 10.1186/1471-2105-11-41, 2828437, 20089173.
    • (2010) BMC Bioinformatics , vol.11 , pp. 41
    • Bordner, A.J.1    Mittelmann, H.D.2
  • 34
    • 48249083459 scopus 로고    scopus 로고
    • Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan
    • 10.1371/journal.pcbi.1000107, 2430535, 18604266
    • Nielsen M, Lundegaard C, Blicher T, Peters B, Sette A, Justesen S, Buus S, Lund O. Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan. PLoS Comput Biol 2008, 4(7):e1000107. [http://dx.plos.org/10.1371%2Fjournal.pcbi.1000107], 10.1371/journal.pcbi.1000107, 2430535, 18604266.
    • (2008) PLoS Comput Biol , vol.4 , Issue.7
    • Nielsen, M.1    Lundegaard, C.2    Blicher, T.3    Peters, B.4    Sette, A.5    Justesen, S.6    Buus, S.7    Lund, O.8
  • 35
    • 0034096818 scopus 로고    scopus 로고
    • IMGT/HLA Database - a sequence database for the human major histocompatibility complex
    • 10.1034/j.1399-0039.2000.550314.x, 10777106
    • Robinson J, Malik A, Parham P, Bodmer J, Marsh S. IMGT/HLA Database - a sequence database for the human major histocompatibility complex. Tissue Antigens 2000, 55(3):280-287. 10.1034/j.1399-0039.2000.550314.x, 10777106.
    • (2000) Tissue Antigens , vol.55 , Issue.3 , pp. 280-287
    • Robinson, J.1    Malik, A.2    Parham, P.3    Bodmer, J.4    Marsh, S.5
  • 36
    • 84877652255 scopus 로고    scopus 로고
    • 2nd machine learning competition in immunology
    • Dana-Farber Cancer Institute
    • Dana-Farber Cancer Institute 2nd machine learning competition in immunology. 2012, [http://bio.dfci.harvard.edu/DFRMLI/HTML/natural.php], Dana-Farber Cancer Institute.
    • (2012)


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.