메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

Dr. PIAS: An integrative system for assessing the druggability of protein-protein interactions

Author keywords

[No Author keywords available]

Indexed keywords

ASSESSMENT SYSTEM; BIOLOGICAL FUNCTIONS; HUMAN IMMUNODEFICIENCY VIRUS; MACHINE-LEARNING; NOVEL METHODOLOGY; PROTEIN-PROTEIN INTERACTIONS; PUBLIC DATABASE; TERTIARY STRUCTURES;

EID: 79651474672     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-50     Document Type: Article
Times cited : (22)

References (56)
  • 1
    • 3142781225 scopus 로고    scopus 로고
    • Small-molecule inhibitors of protein-protein interactions: progressing towards the dream
    • 10.1038/nrd1343, 15060526
    • Arkin MR, Wells JA. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov 2004, 3:301-317. 10.1038/nrd1343, 15060526.
    • (2004) Nat Rev Drug Discov , vol.3 , pp. 301-317
    • Arkin, M.R.1    Wells, J.A.2
  • 2
    • 3342908718 scopus 로고    scopus 로고
    • Emerging classes of protein-protein interaction inhibitors and new tools for their development
    • 10.1016/j.cbpa.2004.06.006, 15288255
    • Pagliaro L, Felding J, Audouze K, Nielsen SJ, Terry RB, Krog-Jensen C, Butcher S. Emerging classes of protein-protein interaction inhibitors and new tools for their development. Curr Opin Chem Biol 2004, 8:442-449. 10.1016/j.cbpa.2004.06.006, 15288255.
    • (2004) Curr Opin Chem Biol , vol.8 , pp. 442-449
    • Pagliaro, L.1    Felding, J.2    Audouze, K.3    Nielsen, S.J.4    Terry, R.B.5    Krog-Jensen, C.6    Butcher, S.7
  • 3
    • 13844275835 scopus 로고    scopus 로고
    • Inhibiting protein-protein interactions using designed molecules
    • 10.1016/j.sbi.2005.01.005, 15718130
    • Zhao L, Chmielewski J. Inhibiting protein-protein interactions using designed molecules. Curr Opin Struct Biol 2005, 15:31-34. 10.1016/j.sbi.2005.01.005, 15718130.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 31-34
    • Zhao, L.1    Chmielewski, J.2
  • 4
    • 37249004920 scopus 로고    scopus 로고
    • Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
    • 10.1038/nature06526, 18075579
    • Wells JA, McClendon CL. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007, 450:1001-1009. 10.1038/nature06526, 18075579.
    • (2007) Nature , vol.450 , pp. 1001-1009
    • Wells, J.A.1    McClendon, C.L.2
  • 6
    • 70349739403 scopus 로고    scopus 로고
    • Assessing the druggability of protein-protein interactions by a supervised machine-learning method
    • 10.1186/1471-2105-10-263, 2755483, 19686586
    • Sugaya N, Ikeda K. Assessing the druggability of protein-protein interactions by a supervised machine-learning method. BMC Bioinformatics 2009, 10:253. 10.1186/1471-2105-10-263, 2755483, 19686586.
    • (2009) BMC Bioinformatics , vol.10 , pp. 253
    • Sugaya, N.1    Ikeda, K.2
  • 7
    • 0036084258 scopus 로고    scopus 로고
    • TTD: Therapeutic Target Database
    • 10.1093/nar/30.1.412, 99057, 11752352
    • Chen X, Ji ZL, Chen YZ. TTD: Therapeutic Target Database. Nucleic Acids Res 2002, 30:412-415. 10.1093/nar/30.1.412, 99057, 11752352.
    • (2002) Nucleic Acids Res , vol.30 , pp. 412-415
    • Chen, X.1    Ji, Z.L.2    Chen, Y.Z.3
  • 9
    • 40549130652 scopus 로고    scopus 로고
    • PDTD: a web-accessible protein database for drug target identification
    • 10.1186/1471-2105-9-104, 2265675, 18282303
    • Gao Z, Li H, Zhang H, Liu X, Kang L, Luo X, Zhu W, Chen K, Wang X, Jiang H. PDTD: a web-accessible protein database for drug target identification. BMC Bioinformatics 2008, 9:104. 10.1186/1471-2105-9-104, 2265675, 18282303.
    • (2008) BMC Bioinformatics , vol.9 , pp. 104
    • Gao, Z.1    Li, H.2    Zhang, H.3    Liu, X.4    Kang, L.5    Luo, X.6    Zhu, W.7    Chen, K.8    Wang, X.9    Jiang, H.10
  • 10
    • 48449090136 scopus 로고    scopus 로고
    • SuperPred: drug classification and target prediction
    • 10.1093/nar/gkn307, 2447784, 18499712
    • Dunkel M, Günther S, Ahmed J, Wittig B, Preissner R. SuperPred: drug classification and target prediction. Nucleic Acids Res 2008, 36:W55-W59. 10.1093/nar/gkn307, 2447784, 18499712.
    • (2008) Nucleic Acids Res , vol.36
    • Dunkel, M.1    Günther, S.2    Ahmed, J.3    Wittig, B.4    Preissner, R.5
  • 11
    • 77949743743 scopus 로고    scopus 로고
    • Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database
    • 10.1371/journal.pone.0009598, 2834754, 20231898
    • Bourgeas R, Basse MJ, Morelli X, Roche P. Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. PLoS ONE 2010, 5:e9598. 10.1371/journal.pone.0009598, 2834754, 20231898.
    • (2010) PLoS ONE , vol.5
    • Bourgeas, R.1    Basse, M.J.2    Morelli, X.3    Roche, P.4
  • 12
    • 70349756972 scopus 로고    scopus 로고
    • Atomic interactions and profile of small molecules disrupting protein-protein interfaces: the TIMBAL database
    • 10.1111/j.1747-0285.2009.00889.x, 19811506
    • Higueruelo AP, Schreyer A, Bickerton GR, Pitt WR, Groom CR, Blundell TL. Atomic interactions and profile of small molecules disrupting protein-protein interfaces: the TIMBAL database. Chem Biol Drug Des 2009, 74:457-467. 10.1111/j.1747-0285.2009.00889.x, 19811506.
    • (2009) Chem Biol Drug Des , vol.74 , pp. 457-467
    • Higueruelo, A.P.1    Schreyer, A.2    Bickerton, G.R.3    Pitt, W.R.4    Groom, C.R.5    Blundell, T.L.6
  • 13
    • 0037061646 scopus 로고    scopus 로고
    • Inhibition of protein-protein association by small molecules: approaches and progress
    • Toogood PL. Inhibition of protein-protein association by small molecules: approaches and progress. J Med Chem 2007, 45:1543-1558.
    • (2007) J Med Chem , vol.45 , pp. 1543-1558
    • Toogood, P.L.1
  • 14
    • 23244448029 scopus 로고    scopus 로고
    • Disruption of protein-protein interactions: towards new targets for chemotherapy
    • 10.1002/jcp.20356, 15880642
    • Loregian A, Palù G. Disruption of protein-protein interactions: towards new targets for chemotherapy. J Cell Physiol 2005, 204:750-762. 10.1002/jcp.20356, 15880642.
    • (2005) J Cell Physiol , vol.204 , pp. 750-762
    • Loregian, A.1    Palù, G.2
  • 15
    • 34447290874 scopus 로고    scopus 로고
    • Protein-protein interaction inhibitors: small molecules from screening techniques
    • 10.2174/156802607780906735, 17508923
    • Fletcher S, Hamilton AD. Protein-protein interaction inhibitors: small molecules from screening techniques. Curr Top Med Chem 2007, 7:922-927. 10.2174/156802607780906735, 17508923.
    • (2007) Curr Top Med Chem , vol.7 , pp. 922-927
    • Fletcher, S.1    Hamilton, A.D.2
  • 16
    • 84865560594 scopus 로고    scopus 로고
    • LIBSVM-A Library for Support Vector Machines-
    • LIBSVM-A Library for Support Vector Machines-. , http://www.csie.ntu.edu.tw/~cjlin/libsvm/
  • 17
    • 33846056843 scopus 로고    scopus 로고
    • Entrez Gene: gene-centered information at NCBI
    • 10.1093/nar/gkl993, 1761442, 17148475
    • Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2007, 35:D26-D31. 10.1093/nar/gkl993, 1761442, 17148475.
    • (2007) Nucleic Acids Res , vol.35
    • Maglott, D.1    Ostell, J.2    Pruitt, K.D.3    Tatusova, T.4
  • 18
    • 65149085556 scopus 로고    scopus 로고
    • Genome Network Platform
    • Genome Network Platform. , http://genomenetwork.nig.ac.jp/download/dataset_e.html
  • 21
    • 42149116826 scopus 로고    scopus 로고
    • A map of human protein interactions derived from co-expression of human mRNAs and their orthologs
    • 10.1038/msb.2008.19, 2387231, 18414481
    • Ramani AK, Li Z, Hart GT, Carlson MW, Boutz DR, Marcotte EM. A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol Syst Biol 2008, 4:180. 10.1038/msb.2008.19, 2387231, 18414481.
    • (2008) Mol Syst Biol , vol.4 , pp. 180
    • Ramani, A.K.1    Li, Z.2    Hart, G.T.3    Carlson, M.W.4    Boutz, D.R.5    Marcotte, E.M.6
  • 22
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • 10.1093/nar/25.17.3389, 146917, 9254694
    • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 24
    • 84873073078 scopus 로고    scopus 로고
    • Chemical Computing Group
    • Chemical Computing Group. , http://www.chemcomp.com/
  • 25
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • 10.1002/bip.360221211, 6667333
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22:2577-2637. 10.1002/bip.360221211, 6667333.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 26
    • 84888279090 scopus 로고    scopus 로고
    • Dr. PIAS Help
    • Dr. PIAS Help. , http://asp.gridasp.net/drpias/pias_help.php
  • 27
    • 13444254300 scopus 로고    scopus 로고
    • PDBsum more: new summaries and analyses of the known 3 D structures of proteins and nucleic acids
    • 10.1093/nar/gki001, 539955, 15608193
    • Laskowski RA, Chistyakov VV, Thornton JM. PDBsum more: new summaries and analyses of the known 3 D structures of proteins and nucleic acids. Nucleic Acids Res 2005, 33:D266-268. 10.1093/nar/gki001, 539955, 15608193.
    • (2005) Nucleic Acids Res , vol.33
    • Laskowski, R.A.1    Chistyakov, V.V.2    Thornton, J.M.3
  • 29
    • 13844264506 scopus 로고    scopus 로고
    • IPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
    • 10.1093/bioinformatics/bti011, 15353450
    • Finn RD, Marshall M, Bateman A. iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 2005, 21:410-412. 10.1093/bioinformatics/bti011, 15353450.
    • (2005) Bioinformatics , vol.21 , pp. 410-412
    • Finn, R.D.1    Marshall, M.2    Bateman, A.3
  • 30
  • 31
    • 38149063767 scopus 로고    scopus 로고
    • Structural disorder promotes assembly of protein complexes
    • 10.1186/1472-6807-7-65, 2194777, 17922903
    • Hegyi H, Schad E, Tompa P. Structural disorder promotes assembly of protein complexes. BMC Struct Biol 2007, 7:65. 10.1186/1472-6807-7-65, 2194777, 17922903.
    • (2007) BMC Struct Biol , vol.7 , pp. 65
    • Hegyi, H.1    Schad, E.2    Tompa, P.3
  • 32
    • 34249695447 scopus 로고    scopus 로고
    • Local structural disorder imparts plasticity on linear motifs
    • 10.1093/bioinformatics/btm035, 17387114
    • Fuxreiter M, Tompa P, Simon I. Local structural disorder imparts plasticity on linear motifs. Bioinformatics 2007, 23:950-956. 10.1093/bioinformatics/btm035, 17387114.
    • (2007) Bioinformatics , vol.23 , pp. 950-956
    • Fuxreiter, M.1    Tompa, P.2    Simon, I.3
  • 33
    • 41149119083 scopus 로고    scopus 로고
    • The role of disorder in interaction networks: a structural analysis
    • Kim PM, Sboner A, Xia Y, Gerstein M. The role of disorder in interaction networks: a structural analysis. Mol Sys Biol 2008, 4:179.
    • (2008) Mol Sys Biol , vol.4 , pp. 179
    • Kim, P.M.1    Sboner, A.2    Xia, Y.3    Gerstein, M.4
  • 35
    • 57049157033 scopus 로고    scopus 로고
    • BCL-2 family antagonists for cancer therapy
    • 10.1038/nrd2658, 19043450
    • Lessene G, Czabotar PE, Colman PM. BCL-2 family antagonists for cancer therapy. Nat Rev Drug Discov 2008, 7:989-1000. 10.1038/nrd2658, 19043450.
    • (2008) Nat Rev Drug Discov , vol.7 , pp. 989-1000
    • Lessene, G.1    Czabotar, P.E.2    Colman, P.M.3
  • 36
    • 3843086358 scopus 로고    scopus 로고
    • Structure-based design, synthesis, and evaluation of conformationally constrained mimetics of the second mitochondria-derived activator of caspase that target the X-linked inhibitor of apoptosis protein/caspase-9 interaction site
    • 10.1021/jm0499108, 15293984
    • Sun H, Nikolovska-Coleska Z, Yang CY, Xu L, Tomita Y, Krajewski K, Roller PP, Wang S. Structure-based design, synthesis, and evaluation of conformationally constrained mimetics of the second mitochondria-derived activator of caspase that target the X-linked inhibitor of apoptosis protein/caspase-9 interaction site. J Med Chem 2004, 47:4147-4150. 10.1021/jm0499108, 15293984.
    • (2004) J Med Chem , vol.47 , pp. 4147-4150
    • Sun, H.1    Nikolovska-Coleska, Z.2    Yang, C.Y.3    Xu, L.4    Tomita, Y.5    Krajewski, K.6    Roller, P.P.7    Wang, S.8
  • 37
    • 34548567232 scopus 로고    scopus 로고
    • POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions
    • 10.1093/bioinformatics/btm302, 17545177
    • Hirose S, Shimizu K, Kanai S, Kuroda Y, Noguchi T. POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions. Bioinformatics 2007, 23:2046-2053. 10.1093/bioinformatics/btm302, 17545177.
    • (2007) Bioinformatics , vol.23 , pp. 2046-2053
    • Hirose, S.1    Shimizu, K.2    Kanai, S.3    Kuroda, Y.4    Noguchi, T.5
  • 39
    • 25444432901 scopus 로고    scopus 로고
    • Biosequence analysis using profile hidden Markov models
    • HMMER
    • HMMER biosequence analysis using profile hidden Markov models. HMMER., http://hmmer.janelia.org/
  • 41
    • 84874758908 scopus 로고    scopus 로고
    • ChEMBL
    • ChEMBL ChEMBL., http://www.ebi.ac.uk/chembldb/index.php
  • 42
    • 13444266370 scopus 로고    scopus 로고
    • Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
    • 10.1093/nar/gki033, 539987, 15608251
    • Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005, 33:D514-D517. 10.1093/nar/gki033, 539987, 15608251.
    • (2005) Nucleic Acids Res , vol.33
    • Hamosh, A.1    Scott, A.F.2    Amberger, J.S.3    Bocchini, C.A.4    McKusick, V.A.5
  • 43
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • 10.1093/nar/gkp896, 2808910, 19880382
    • Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010, 38:D355-D360. 10.1093/nar/gkp896, 2808910, 19880382.
    • (2010) Nucleic Acids Res , vol.38
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 45
    • 75849158230 scopus 로고    scopus 로고
    • The Gene Ontology in 2010: extentions and refinements
    • 10.1093/nar/gkp1018, 2808930, 19920128, The Gene Ontology Consortium
    • The Gene Ontology Consortium The Gene Ontology in 2010: extentions and refinements. Nucleic Acids Res 2010, 38:D331-D335. 10.1093/nar/gkp1018, 2808930, 19920128, The Gene Ontology Consortium.
    • (2010) Nucleic Acids Res , vol.38
  • 46
    • 3042855210 scopus 로고    scopus 로고
    • UniGene: a unified view of the transcriptome
    • Bethesda(MD): National Center for Biotechnology Information
    • Pontius JU, Wagner L, Schuler GD. UniGene: a unified view of the transcriptome. The NCBI Handbook 2003, Bethesda(MD): National Center for Biotechnology Information.
    • (2003) The NCBI Handbook
    • Pontius, J.U.1    Wagner, L.2    Schuler, G.D.3
  • 48
    • 34548358584 scopus 로고    scopus 로고
    • EXpanda: an integrated platform for network analysis and visualization
    • Negishi Y, Nakamura H, Yachie N, Saito R, Tomita M. eXpanda: an integrated platform for network analysis and visualization. In Silico Biol 2007, 7:141-144.
    • (2007) In Silico Biol , vol.7 , pp. 141-144
    • Negishi, Y.1    Nakamura, H.2    Yachie, N.3    Saito, R.4    Tomita, M.5
  • 49
    • 84870435682 scopus 로고    scopus 로고
    • Jmol: an open-source Java viewer for chemical structures in 3 D
    • Jmol: an open-source Java viewer for chemical structures in 3 D. , http://jmol.sourceforge.net/
  • 51
    • 75549083827 scopus 로고    scopus 로고
    • EGFR signaling and drug discovery
    • 10.1159/000279388, 20130423
    • Lurje G, Lenz H-J. EGFR signaling and drug discovery. Oncology 2009, 77:400-410. 10.1159/000279388, 20130423.
    • (2009) Oncology , vol.77 , pp. 400-410
    • Lurje, G.1    Lenz, H.-J.2
  • 52
    • 67650473470 scopus 로고    scopus 로고
    • Recent advances of novel targeted therapy in non-small cell lung cancer
    • 10.1186/1756-8722-2-2, 2637898, 19159467
    • Katzel JA, Fanucchi MP, Li Z. Recent advances of novel targeted therapy in non-small cell lung cancer. J Hematol Oncol 2009, 2:2. 10.1186/1756-8722-2-2, 2637898, 19159467.
    • (2009) J Hematol Oncol , vol.2 , pp. 2
    • Katzel, J.A.1    Fanucchi, M.P.2    Li, Z.3
  • 53
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • 10.1006/jmbi.1998.1843, 9653027
    • Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol 1998, 280:1-9. 10.1006/jmbi.1998.1843, 9653027.
    • (1998) J Mol Biol , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 54
    • 0036093538 scopus 로고    scopus 로고
    • Analysis of homodimeric protein interfaces by graph-spectral methods
    • 10.1093/protein/15.4.265, 11983927
    • Brinda KV, Kannan N, Vishveshwara S. Analysis of homodimeric protein interfaces by graph-spectral methods. Protein Eng 2002, 15:265-277. 10.1093/protein/15.4.265, 11983927.
    • (2002) Protein Eng , vol.15 , pp. 265-277
    • Brinda, K.V.1    Kannan, N.2    Vishveshwara, S.3
  • 55
    • 33646104191 scopus 로고    scopus 로고
    • Molecular targeting of growth factor receptor-bound 2 (Grb2) as an anti-cancer strategy
    • 10.1097/01.cad.0000185180.72604.ac, 16317285
    • Dharmawardana PG, Peruzzi B, Giubellino A, Burke TR, Bottaro DP. Molecular targeting of growth factor receptor-bound 2 (Grb2) as an anti-cancer strategy. Anticancer Drugs 2006, 17:13-20. 10.1097/01.cad.0000185180.72604.ac, 16317285.
    • (2006) Anticancer Drugs , vol.17 , pp. 13-20
    • Dharmawardana, P.G.1    Peruzzi, B.2    Giubellino, A.3    Burke, T.R.4    Bottaro, D.P.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.