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Volumn 5, Issue 5, 2009, Pages

Drug discovery using chemical systems biology: Identification of the protein-ligand binding network to explain the side effects of CETP inhibitors

Author keywords

[No Author keywords available]

Indexed keywords

DISEASE CONTROL; DISEASES; LIGANDS; PROTEINS;

EID: 67049100457     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000387     Document Type: Article
Times cited : (243)

References (106)
  • 2
    • 1642540579 scopus 로고    scopus 로고
    • Unexpected Nanomolar Inhibition of Carbonic Anhydrase by COX-2-Selective Celecoxib: New Pharmacological Opportunities Due to Related Binding Site Recognition
    • DOI 10.1021/jm030912m
    • Weber A, Casini A, Heine A, Kuhn D, Supuran CT, et al. (2004) Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition. J Med Chem 47: 550-557. (Pubitemid 38129713)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.3 , pp. 550-557
    • Weber, A.1    Casini, A.2    Heine, A.3    Kuhn, D.4    Supuran, C.T.5    Scozzafava, A.6    Klebe, G.7
  • 4
    • 36949009488 scopus 로고    scopus 로고
    • In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators
    • doi:10.1371/journal.pcbi.0030217
    • Xie L, Wang J, Bourne PE (2007) In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comp Biol 3: e217. doi:10.1371/journal.pcbi.0030217.
    • (2007) PLoS Comp Biol , vol.3
    • Xie, L.1    Wang, J.2    Bourne, P.E.3
  • 6
    • 33845762340 scopus 로고    scopus 로고
    • Multi-target therapeutics: When the whole is greater than the sum of the parts
    • DOI 10.1016/j.drudis.2006.11.008, PII S1359644606004697
    • Zimmermann GR, Lehár J, Keith CT (2007) Multi-target therapeutics: when the whole is greater than the sum of the parts. Drug Discov Today 12: 34-42. (Pubitemid 46014485)
    • (2007) Drug Discovery Today , vol.12 , Issue.1-2 , pp. 34-42
    • Zimmermann, G.R.1    Lehar, J.2    Keith, C.T.3
  • 7
    • 33644668387 scopus 로고    scopus 로고
    • Finding new tricks for old drugs: An efficient route for public-sector drug discovery
    • O'Connor KA, Roth BL (2005) Finding new tricks for old drugs: an efficient route for public-sector drug discovery. Nat Rev Drug Discov 4: 1005-1014.
    • (2005) Nat Rev Drug Discov , vol.4 , pp. 1005-1014
    • O'Connor, K.A.1    Roth, B.L.2
  • 8
    • 4344668661 scopus 로고    scopus 로고
    • Drug repositioning: Identifying and developing new uses for existing drugs
    • Ashburn TT, Thor KB (2004) Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov 3: 673-683. (Pubitemid 39173508)
    • (2004) Nature Reviews Drug Discovery , vol.3 , Issue.8 , pp. 673-683
    • Ashburn, T.T.1    Thor, K.B.2
  • 9
    • 0030886937 scopus 로고    scopus 로고
    • Managing the drug discovery/development interface
    • DOI 10.1016/S1359-6446(97)01099-4, PII S1359644697010994
    • Kennedy T (1997) Managing the drug discovery /development interface. Drug Discov Today 2: 436-444. (Pubitemid 27387353)
    • (1997) Drug Discovery Today , vol.2 , Issue.10 , pp. 436-444
    • Kennedy, T.1
  • 10
    • 33747620519 scopus 로고    scopus 로고
    • Systems biology and combination therapy in the quest for clinical efficacy
    • DOI 10.1038/nchembio817, PII NCHEMBIO817
    • Fitzgerald JB, Schoeberl B, Nielsen UB, Sorger PK (2006) Systems biology and combination therapy in the quest for clinical efficacy. Nat Chem Biol 2: 458-466. (Pubitemid 44266307)
    • (2006) Nature Chemical Biology , vol.2 , Issue.9 , pp. 458-466
    • Fitzgerald, J.B.1    Schoeberl, B.2    Nielsen, U.B.3    Sorger, P.K.4
  • 11
    • 47249146126 scopus 로고    scopus 로고
    • Drug target identification using side-effect similarity
    • DOI 10.1126/science.1158140
    • Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P (2008) Drug target identification using side-effect similarity. Science 321: 263-266. (Pubitemid 351989100)
    • (2008) Science , vol.321 , Issue.5886 , pp. 263-266
    • Campillos, M.1    Kuhn, M.2    Gavin, A.-C.3    Jensen, L.J.4    Bork, P.5
  • 13
    • 33745661919 scopus 로고    scopus 로고
    • Chemogenomics: Drug discovery's panacea?
    • Jacoby E (2006) Chemogenomics: drug discovery's panacea? Mol Biosyst 2: 218-220.
    • (2006) Mol Biosyst , vol.2 , pp. 218-220
    • Jacoby, E.1
  • 14
    • 4043121114 scopus 로고    scopus 로고
    • Computational chemogenomics approaches to systematic knowledge-based drug discovery
    • Mestres J (2004) Computational chemogenomics approaches to systematic knowledge-based drug discovery. Curr Opin Drug Discov Devel 7: 304-313. (Pubitemid 44120947)
    • (2004) Current Opinion in Drug Discovery and Development , vol.7 , Issue.3 , pp. 304-313
    • Mestres, J.1
  • 15
    • 34548317031 scopus 로고    scopus 로고
    • Chemogenomic approaches to rational drug design
    • DOI 10.1038/sj.bjp.0707307, PII 0707307
    • Rognan D (2007) Chemogenomic approaches to rational drug design. Br J Pharmacol 152: 38-52. (Pubitemid 47339898)
    • (2007) British Journal of Pharmacology , vol.152 , Issue.1 , pp. 38-52
    • Rognan, D.1
  • 16
    • 3342907009 scopus 로고    scopus 로고
    • Exploring the chemogenomic knowledge space with annotated chemical libraries
    • DOI 10.1016/j.cbpa.2004.06.003, PII S1367593104000791
    • Savchuk NP, Balakin KV, Tkachenko SE (2004) Exploring the chemogenomic knowledge space with annotated chemical libraries. Curr Opin Chem Biol 8: 414-417. (Pubitemid 38993735)
    • (2004) Current Opinion in Chemical Biology , vol.8 , Issue.4 , pp. 412-417
    • Savchuk, N.P.1    Balakin, K.V.2    Tkachenko, S.E.3
  • 17
    • 41949132102 scopus 로고    scopus 로고
    • Chemogenomics and biotechnology
    • Wuster A, Madan Babu M (2008) Chemogenomics and biotechnology. Trends Biotechnol 26: 252-258.
    • (2008) Trends Biotechnol , vol.26 , pp. 252-258
    • Wuster, A.1    Madan Babu, M.2
  • 18
    • 44449159422 scopus 로고    scopus 로고
    • Quantifying the relationships among drug classes
    • Hert, Keiser, Irwin, Oprea, Shoichet (2008) Quantifying the relationships among drug classes. J Chem Inf Model 48: 755-765.
    • (2008) J Chem Inf Model , vol.48 , pp. 755-765
    • Hert1    Keiser2    Irwin3    Oprea4    Shoichet5
  • 19
    • 34447645811 scopus 로고    scopus 로고
    • A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites
    • DOI 10.1186/1471-2105-8-S4-S9
    • Xie L, Bourne PE (2007) A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinformatics 8: S9. (Pubitemid 351833828)
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 4
    • Xie, L.1    Bourne, P.E.2
  • 20
    • 44449139387 scopus 로고    scopus 로고
    • Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
    • DOI 10.1073/pnas.0704422105
    • Xie L, Bourne PE (2008) Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A 105: 5441-5446. (Pubitemid 351753882)
    • (2008) Proceedings of the National Academy of Sciences of the United States of America , vol.105 , Issue.14 , pp. 5441-5446
    • Xie, L.1    Bourne, P.E.2
  • 22
    • 48149106322 scopus 로고    scopus 로고
    • Torcetrapib-induced blood pressure elevation is independent of CETP inhibition and is accompanied by increased circulating levels of aldosterone
    • Forrest MJ, Bloomfield D, Briscoe RJ, Brown PN, Cumiskey A-M, et al. (2008) Torcetrapib-induced blood pressure elevation is independent of CETP inhibition and is accompanied by increased circulating levels of aldosterone. Br J Pharmacol 154: 1465-1473.
    • (2008) Br J Pharmacol , vol.154 , pp. 1465-1473
    • Forrest, M.J.1    Bloomfield, D.2    Briscoe, R.J.3    Brown, P.N.4    Cumiskey, A.-M.5
  • 23
    • 35248878864 scopus 로고    scopus 로고
    • The withdrawal of torcetrapib from drug development: Implications for the future of drugs that alter HDL metabolism
    • DOI 10.1517/13543784.16.10.1509
    • Howes LG, Kostner K (2007) The withdrawal of torcetrapib from drug development: implications for the future of drugs that alter HDL metabolism. Expert Opin Investig Drugs 16: 1509-1516. (Pubitemid 350028403)
    • (2007) Expert Opinion on Investigational Drugs , vol.16 , Issue.10 , pp. 1509-1516
    • Howes, L.G.1    Kostner, K.2
  • 24
    • 48149083115 scopus 로고    scopus 로고
    • The failure of torcetrapib: What have we learned?
    • Joy TR, Hegele RA (2008) The failure of torcetrapib: what have we learned? Br J Pharmacol 154: 1379-1381.
    • (2008) Br J Pharmacol , vol.154 , pp. 1379-1381
    • Joy, T.R.1    Hegele, R.A.2
  • 25
    • 44449145644 scopus 로고    scopus 로고
    • Spotlight on HDL-raising therapies: Insights from the torcetrapib trials
    • DOI 10.1038/ncpcardio1191, PII NCPCARDIO1191
    • Kontush A, Guérin M, Chapman MJ (2008) Spotlight on HDL-raising therapies: insights from the torcetrapib trials. Nat Clin Pract Cardiovasc Med 5: 329-336. (Pubitemid 351761707)
    • (2008) Nature Clinical Practice Cardiovascular Medicine , vol.5 , Issue.6 , pp. 329-336
    • Kontush, A.1    Guerin, M.2    Chapman, M.J.3
  • 26
    • 24644451250 scopus 로고    scopus 로고
    • waf1 pathways
    • DOI 10.1016/j.atherosclerosis.2005.02.017, PII S0021915005001577
    • Miura S, Matsuo Y, Kawamura A, Saku K (2005) JTT-705 blocks cell proliferation and angiogenesis through p38 kinase/p27(kip1) and Ras/ p21(waf1) pathways. Atherosclerosis 182: 267-275. (Pubitemid 41267194)
    • (2005) Atherosclerosis , vol.182 , Issue.2 , pp. 267-275
    • Miura, S.-I.1    Matsuo, Y.2    Kawamura, A.3    Saku, K.4
  • 27
    • 34247343346 scopus 로고    scopus 로고
    • Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
    • DOI 10.1007/s10822-007-9114-2
    • Jain AN (2007) Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J Comput Aided Mol Des 21: 281-306. (Pubitemid 46630055)
    • (2007) Journal of Computer-Aided Molecular Design , vol.21 , Issue.5 , pp. 281-306
    • Jain, A.N.1
  • 33
    • 3042581007 scopus 로고    scopus 로고
    • Flexible structure alignment by chaining aligned fragment pairs allowing twists
    • DOI 10.1093/bioinformatics/btg1086
    • Ye Y, Godzik A (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19: ii246-ii255. (Pubitemid 41296662)
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Ye, Y.1    Godzik, A.2
  • 34
    • 47949094965 scopus 로고    scopus 로고
    • Integration of metabolism and inflammation by lipid-activated nuclear receptors
    • Bensinger SJ, Tontonoz P (2008) Integration of metabolism and inflammation by lipid-activated nuclear receptors. Nature 454: 470-477.
    • (2008) Nature , vol.454 , pp. 470-477
    • Bensinger, S.J.1    Tontonoz, P.2
  • 36
    • 38549159946 scopus 로고    scopus 로고
    • FunSimMat: A comprehensive functional similarity database
    • DOI 10.1093/nar/gkm806
    • Schlicker A, Albrecht M (2008) FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res 36: D434-D439. (Pubitemid 351149762)
    • (2008) Nucleic Acids Research , vol.36 , Issue.SUPPL. 1
    • Schlicker, A.1    Albrecht, M.2
  • 37
    • 0002016474 scopus 로고    scopus 로고
    • Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language
    • Resnik P (1999) Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language. Artif Intell Res 11: 95-130. (Pubitemid 129628761)
    • (1999) Journal of Artificial Intelligence Research , vol.11 , pp. 95-130
    • Resnik, P.1
  • 38
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • DOI 10.1021/jm0203783
    • Wang R, Lu Y, Wang S (2003) Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem 46: 2287-2303. (Pubitemid 36637914)
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.12 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 42
    • 45849132015 scopus 로고    scopus 로고
    • Nuclear hormone receptors as regulators of the renin-angiotensin- aldosterone system
    • Kuipers I, van der Harst P, Navis G, van Genne L, Morello F, et al. (2008) Nuclear hormone receptors as regulators of the renin-angiotensin- aldosterone system. Hypertension 51: 1442-1448.
    • (2008) Hypertension , vol.51 , pp. 1442-1448
    • Kuipers, I.1    Van Der Harst, P.2    Navis, G.3    Van Genne, L.4    Morello, F.5
  • 45
    • 0034693323 scopus 로고    scopus 로고
    • Oxidized low density lipoprotein inhibits interleukin-12 production in lipopolysaccharide-activated mouse macrophages via direct interactions between peroxisome proliferator-activated receptor-gamma and nuclear factor-kappa B
    • Chung SW, Kang BY, Kim SH, Pak YK, Cho D, et al. (2000) Oxidized low density lipoprotein inhibits interleukin-12 production in lipopolysaccharide- activated mouse macrophages via direct interactions between peroxisome proliferator-activated receptor-gamma and nuclear factor-kappa B. J Biol Chem 275: 32681-32687.
    • (2000) J Biol Chem , vol.275 , pp. 32681-32687
    • Chung, S.W.1    Kang, B.Y.2    Kim, S.H.3    Pak, Y.K.4    Cho, D.5
  • 46
    • 0034965832 scopus 로고    scopus 로고
    • AP-1-glucocorticoid receptor crosstalk taken to a higher level
    • DOI 10.1677/joe.0.1690447
    • Karin M, Chang L (2001) AP-1-glucocorticoid receptor crosstalk taken to a higher level. J Endocrinol 169: 447-451. (Pubitemid 32536977)
    • (2001) Journal of Endocrinology , vol.169 , Issue.3 , pp. 447-451
    • Karin, M.1    Chang, L.2
  • 47
    • 0034665748 scopus 로고    scopus 로고
    • The glucocorticoid receptor inhibits NFκB by interfering with serine-2 phosphorylation of the RNA polymerase II carboxy-terminal domain
    • DOI 10.1101/gad.827900
    • Nissen RM, Yamamoto KR (2000) The glucocorticoid receptor inhibits NF kappa B by interfering with serine-2 phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev 14: 2314-2329. (Pubitemid 30746014)
    • (2000) Genes and Development , vol.14 , Issue.18 , pp. 2314-2329
    • Nissen, R.M.1    Yamamoto, K.R.2
  • 48
    • 33645284772 scopus 로고    scopus 로고
    • Neural regulation of innate immunity: A coordinated nonspecific host response to pathogens
    • Sternberg EM (2006) Neural regulation of innate immunity: a coordinated nonspecific host response to pathogens. Nat Rev Immunol 6: 318-328.
    • (2006) Nat Rev Immunol , vol.6 , pp. 318-328
    • Sternberg, E.M.1
  • 49
    • 0037324340 scopus 로고    scopus 로고
    • Reciprocal regulation of inflammation and lipid metabolism by liver X receptors
    • DOI 10.1038/nm820
    • Joseph SB, Castrillo A, Laffitte BA, Mangelsdorf DJ, Tontonoz P (2003) Reciprocal regulation of inflammation and lipid metabolism by liver X receptors. Nat Med 9: 213-219. (Pubitemid 36227724)
    • (2003) Nature Medicine , vol.9 , Issue.2 , pp. 213-219
    • Joseph, S.B.1    Castrillo, A.2    Laffitte, B.A.3    Mangelsdorf, D.J.4    Tontonoz, P.5
  • 50
    • 0034121698 scopus 로고    scopus 로고
    • Peroxisome proliferator-activated receptor γ-dependent repression of the inducible nitric oxide synthase gene
    • DOI 10.1128/MCB.20.13.4699-4707.2000
    • Li M, Pascual G, Glass CK (2000) Peroxisome proliferator-activated receptor gamma-dependent repression of the inducible nitric oxide synthase gene. Mol Cell Biol 20: 4699-4707. (Pubitemid 30396117)
    • (2000) Molecular and Cellular Biology , vol.20 , Issue.13 , pp. 4699-4707
    • Li, M.1    Pascual, G.2    Glass, C.K.3
  • 52
    • 0242497709 scopus 로고    scopus 로고
    • Erratum: Transcriptional repression of atherogenic inflammation: Modulation by PPARδ (Science (October 17) (453))
    • Lee CH, Curtiss LK (2003) Transcriptional repression of atherogenic inflammation: Modulation by PPAR delta (vol 302, pg 453, 2003). Science 302: 1153. (Pubitemid 37421001)
    • (2003) Science , vol.302 , Issue.5648 , pp. 1153
    • Lee, C.-H.1    Curtiss, L.K.2
  • 56
    • 33846570444 scopus 로고    scopus 로고
    • The Transcription Factor Nuclear Factor-kappa B and Cancer
    • DOI 10.1016/j.clon.2006.11.013, PII S0936655506004274
    • Escarcega RO, Fuentes-Alexandro S, Garcia-Carrasco M, Gatica A, Zamora A (2007) The transcription factor nuclear factor-kappa B and cancer. Clin Oncol (R Coll Radiol) 19: 154-161. (Pubitemid 46172840)
    • (2007) Clinical Oncology , vol.19 , Issue.2 , pp. 154-161
    • Escarcega, R.O.1    Fuentes-Alexandro, S.2    Garcia-Carrasco, M.3    Gatica, A.4    Zamora, A.5
  • 58
    • 0344443788 scopus 로고    scopus 로고
    • Dependence of Peroxisome Proliferator-activated Receptor Ligand-induced Mitogen-activated Protein Kinase Signaling on Epidermal Growth Factor Receptor Transactivation
    • DOI 10.1074/jbc.M307827200
    • Gardner OS, Dewar BJ, Earp HS, Samet JM, Graves LM (2003) Dependence of peroxisome proliferator-activated receptor ligand-induced mitogen-activated protein kinase signaling on epidermal growth factor receptor transactivation. J Biol Chem 278: 46261-46269. (Pubitemid 37452196)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.47 , pp. 46261-46269
    • Gardner, O.S.1    Dewar, B.J.2    Earp, H.S.3    Samet, J.M.4    Graves, L.M.5
  • 59
    • 34547138678 scopus 로고    scopus 로고
    • Peroxisomal proliferator-activated receptor-α-dependent inhibition of endothelial cell proliferation and tumorigenesis
    • DOI 10.1074/jbc.M701429200
    • Pozzi A, Ibanez MR, Gatica AE, Yang S, Wei S, et al. (2007) Peroxisomal proliferator-activated receptor-alpha-dependent inhibition of endothelial cell proliferation and tumorigenesis. J Biol Chem 282: 17685-17695. (Pubitemid 47100312)
    • (2007) Journal of Biological Chemistry , vol.282 , Issue.24 , pp. 17685-17695
    • Pozzi, A.1    Ibanez, M.R.2    Gatica, A.E.3    Yang, S.4    Wei, S.5    Mei, S.6    Falck, J.R.7    Capdevila, J.H.8
  • 60
    • 0035282334 scopus 로고    scopus 로고
    • Mammalian MAP kinase signalling cascades
    • DOI 10.1038/35065000
    • Chang L, Karin M (2001) Mammalian MAP kinase signalling cascades. Nature 410: 37-40. (Pubitemid 32225829)
    • (2001) Nature , vol.410 , Issue.6824 , pp. 37-40
    • Chang, L.1    Karin, M.2
  • 61
    • 44449118921 scopus 로고    scopus 로고
    • Fatty acid-binding proteins: Role in metabolic diseases and potential as drug targets
    • DOI 10.1038/nrd2589, PII NRD2589
    • Furuhashi M, Hotamisligil GS (2008) Fatty acid-binding proteins: role in metabolic diseases and potential as drug targets. Nat Rev Drug Discov 7: 489-503. (Pubitemid 351767117)
    • (2008) Nature Reviews Drug Discovery , vol.7 , Issue.6 , pp. 489-503
    • Furuhashi, M.1    Hotamisligil, G.S.2
  • 62
    • 0035956863 scopus 로고    scopus 로고
    • Fatty acids and hypolipidemic drugs regulate peroxisome proliferator-activated receptors α- And γ-mediated gene expression via liver fatty acid binding protein: A signaling path to the nucleus
    • DOI 10.1073/pnas.051619898
    • Wolfrum C, Borrmann CM, Borchers T, Spener F (2001) Fatty acids and hypolipidemic drugs regulate peroxisome proliferator-activated receptors alpha- and gamma-mediated gene expression via liver fatty acid binding protein: a signaling path to the nucleus. Proc Natl Acad Sci U S A 98: 2323-2328. (Pubitemid 32209481)
    • (2001) Proceedings of the National Academy of Sciences of the United States of America , vol.98 , Issue.5 , pp. 2323-2328
    • Wolfrum, C.1    Borrmann, C.M.2    Borchers, T.3    Spener, F.4
  • 63
    • 3242733220 scopus 로고    scopus 로고
    • Functional analysis of peroxisome-proliferator-responsive element motifs in genes of fatty acid-binding proteins
    • DOI 10.1042/BJ20031340
    • Schachtrup C, Emmler T, Bleck B, Sandqvist A, Spener F (2004) Functional analysis of peroxisome-proliferator-responsive element motifs in genes of fatty acid-binding proteins. Biochem J 382: 239-245. (Pubitemid 39141587)
    • (2004) Biochemical Journal , vol.382 , Issue.1 , pp. 239-245
    • Schachtrup, C.1    Emmler, T.2    Bleck, B.3    Sandqvist, A.4    Spener, F.5
  • 64
    • 0036291635 scopus 로고    scopus 로고
    • Selective cooperation between fatty acid binding proteins and peroxisome proliferator-activated receptors in regulating transcription
    • DOI 10.1128/MCB.22.14.5114-5127.2002
    • Tan N-S, Shaw NS, Vinckenbosch N, Liu P, Yasmin R, et al. (2002) Selective cooperation between fatty acid binding proteins and peroxisome proliferator-activated receptors in regulating transcription. Mol Cell Biol 22: 5114-5127. (Pubitemid 34700702)
    • (2002) Molecular and Cellular Biology , vol.22 , Issue.14 , pp. 5114-5127
    • Tan, N.-S.1    Shaw, N.S.2    Vinckenbosch, N.3    Liu, P.4    Yasmin, R.5    Desvergne, B.6    Wahli, W.7    Noy, N.8
  • 65
    • 0034523480 scopus 로고    scopus 로고
    • CD1 proteins: Targets of T cell recognition in innate and adaptive immunity
    • Ulrichs T, Porcelli SA (2000) CD1 proteins: targets of T cell recognition in innate and adaptive immunity. Rev Immunogenet 2: 416-432. (Pubitemid 32041165)
    • (2000) Reviews in Immunogenetics , vol.2 , Issue.3 , pp. 416-432
    • Ulrichs, T.1    Porcelli, S.A.2
  • 66
    • 38049005316 scopus 로고    scopus 로고
    • Ubiquinol-cytochrome-c reductase 7.2 kDa protein of mitochondrial complex III is steroid-responsive and increases in cardiac hypertrophy and hypertension
    • Huynh H, Servant N, Chalifour LE (2007) Ubiquinol-cytochrome-c reductase 7.2 kDa protein of mitochondrial complex III is steroid-responsive and increases in cardiac hypertrophy and hypertension. Can J Physiol Pharmacol 85: 986-996.
    • (2007) Can J Physiol Pharmacol , vol.85 , pp. 986-996
    • Huynh, H.1    Servant, N.2    Chalifour, L.E.3
  • 67
    • 0025358947 scopus 로고
    • 1 complex
    • Trumpower BL (1990) The protonmotive Q-cycle: energy transduction by coupling of proton translocation to electron-transfer by the cytochrome-bc1 complex. J Biol Chem 265: 11409-11412. (Pubitemid 20219292)
    • (1990) Journal of Biological Chemistry , vol.265 , Issue.20 , pp. 11409-11412
    • Trumpower, B.L.1
  • 68
    • 0016754421 scopus 로고
    • The protonmotive Q cycle: A general formulation
    • Mitchell P (1975) The protonmotive Q cycle: a general formulation. FEBS Lett 59: 137-139.
    • (1975) FEBS Lett , vol.59 , pp. 137-139
    • Mitchell, P.1
  • 69
    • 0032570577 scopus 로고    scopus 로고
    • Cytochrome c in the apoptotic and antioxidant cascades
    • DOI 10.1016/S0014-5793(98)00061-1, PII S0014579398000611
    • Skulachev VP (1998) Cytochrome c in the apoptotic and antioxidant cascades. FEBS Lett 423: 275-280. (Pubitemid 28129349)
    • (1998) FEBS Letters , vol.423 , Issue.3 , pp. 275-280
    • Skulachev, V.P.1
  • 70
    • 49649108349 scopus 로고    scopus 로고
    • Hemoglobin is expressed by mesangial cells and reduces oxidant stress
    • Nishi H, Inagi R, Kato H, Tanemoto M, Kojima I, et al. (2008) Hemoglobin is expressed by mesangial cells and reduces oxidant stress. J Am Soc Nephrol 19: 1500-1508.
    • (2008) J Am Soc Nephrol , vol.19 , pp. 1500-1508
    • Nishi, H.1    Inagi, R.2    Kato, H.3    Tanemoto, M.4    Kojima, I.5
  • 72
    • 1542343934 scopus 로고    scopus 로고
    • Expression of HbC and HbS, but not HbA, results in activation of K-Cl cotransport activity in transgenic mouse red cells
    • DOI 10.1182/blood-2003-01-0237
    • Romero JR, Suzuka SM, Nagel RL, Fabry ME (2004) Expression of HbC and HbS, but not HbA, results in activation of K-Cl cotransport activity in transgenic mouse red cells. Blood 103: 2384-2390. (Pubitemid 38326262)
    • (2004) Blood , vol.103 , Issue.6 , pp. 2384-2390
    • Romero, J.R.1    Suzuka, S.M.2    Nagel, R.L.3    Fabry, M.E.4
  • 73
    • 42049093998 scopus 로고    scopus 로고
    • Endothelial S100A1 modulates vascular function via nitric oxide
    • Pleger ST, Harris DM, Shan C, Vinge LE, Chuprun JK, et al. (2008) Endothelial S100A1 modulates vascular function via nitric oxide. Circ Res 102: 786-794.
    • (2008) Circ Res , vol.102 , pp. 786-794
    • Pleger, S.T.1    Harris, D.M.2    Shan, C.3    Vinge, L.E.4    Chuprun, J.K.5
  • 74
    • 0035996798 scopus 로고    scopus 로고
    • The role of calcium-binding proteins in the control of transcription: Structure to function
    • DOI 10.1002/bies.10105
    • Ikura M, Osawa M, Ames JB (2002) The role of calcium-binding proteins in the control of transcription: structure to function. Bioessays 24: 625-636. (Pubitemid 34780350)
    • (2002) BioEssays , vol.24 , Issue.7 , pp. 625-636
    • Ikura, M.1    Osawa, M.2    Ames, J.B.3
  • 76
    • 2342618157 scopus 로고    scopus 로고
    • Biological functions of phosphatidylinositol transfer proteins
    • DOI 10.1139/o03-089
    • Routt SM, Bankaitis VA (2004) Biological functions of phosphatidylinositol transfer proteins. Biochem Cell Biol 82: 254-262. (Pubitemid 38580886)
    • (2004) Biochemistry and Cell Biology , vol.82 , Issue.1 , pp. 254-262
    • Routt, S.M.1    Bankaitis, V.A.2
  • 77
    • 38549106408 scopus 로고    scopus 로고
    • Mechanisms of exocytosis
    • DOI 10.1111/j.1748-1716.2007.01803.x
    • Sugita S (2008) Mechanisms of exocytosis. Acta Physiol (Oxf) 192: 185-193. (Pubitemid 351160988)
    • (2008) Acta Physiologica , vol.192 , Issue.2 , pp. 185-193
    • Sugita, S.1
  • 78
    • 15544377794 scopus 로고    scopus 로고
    • Molecular and evolutionary basis of the cellular stress response
    • DOI 10.1146/annurev.physiol.67.040403.103635
    • Kültz D (2005) Molecular and evolutionary basis of the cellular stress response. Annu Rev Physiol 67: 225-257. (Pubitemid 40404492)
    • (2005) Annual Review of Physiology , vol.67 , pp. 225-257
    • Kultz, D.1
  • 79
    • 0038504995 scopus 로고    scopus 로고
    • Lipids and the immune response: From molecular mechanisms to clinical applications
    • DOI 10.1097/00075197-200303000-00002
    • Yaqoob P (2003) Lipids and the immune response: from molecular mechanisms to clinical applications. Curr Opin Clin Nutr Metab Care 6: 133-150. (Pubitemid 40674517)
    • (2003) Current Opinion in Clinical Nutrition and Metabolic Care , vol.6 , Issue.2 , pp. 133-150
    • Yaqoob, P.1
  • 80
    • 1842680755 scopus 로고    scopus 로고
    • Membrane lipids and cell death: An overview
    • DOI 10.1016/j.chemphyslip.2004.02.002, PII S0009308404000143
    • Cristea IM, Degli Esposti M (2004) Membrane lipids and cell death: an overview. Chem Phys Lipids 129: 133-160. (Pubitemid 38476987)
    • (2004) Chemistry and Physics of Lipids , vol.129 , Issue.2 , pp. 133-160
    • Cristea, I.M.1    Degli Esposti, M.2
  • 81
    • 30944434575 scopus 로고    scopus 로고
    • Cross-talk between IGF-I and TGF-β signaling pathways
    • DOI 10.1016/j.cytogfr.2005.09.007, PII S1359610105001115
    • Danielpour D, Song K (2006) Cross-talk between IGF-I and TGF-beta signaling pathways. Cytokine Growth Factor Rev 17: 59-74. (Pubitemid 43117516)
    • (2006) Cytokine and Growth Factor Reviews , vol.17 , Issue.1-2 , pp. 59-74
    • Danielpour, D.1    Song, K.2
  • 82
    • 55449107518 scopus 로고    scopus 로고
    • Functional coverage of the human genome by existing structures, structural genomics targets, and homology models
    • doi:10.1371/journal.pcbi.0010031
    • Xie L, Bourne PE (2005) Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comp Biol 1: e31. doi:10.1371/journal.pcbi.0010031.
    • (2005) PLoS Comp Biol , vol.1
    • Xie, L.1    Bourne, P.E.2
  • 84
    • 2442614144 scopus 로고    scopus 로고
    • Recognition of functional sites in protein structures
    • DOI 10.1016/j.jmb.2004.04.012, PII S0022283604004139
    • Shulman-Peleg A, Nussinov R, Wolfson HJ (2004) Recognition of functional sites in protein structures. J Mol Biol 339: 607-633. (Pubitemid 38625909)
    • (2004) Journal of Molecular Biology , vol.339 , Issue.3 , pp. 607-633
    • Shulman-Peleg, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 85
    • 33644876699 scopus 로고    scopus 로고
    • SitesBase: A database for structure-based protein-ligand binding site comparisons
    • Gold ND, Jackson RM (2006) SitesBase: a database for structure-based protein-ligand binding site comparisons. Nucleic Acids Res 34: D231-234.
    • (2006) Nucleic Acids Res , vol.34
    • Gold, N.D.1    Jackson, R.M.2
  • 86
    • 33646254603 scopus 로고    scopus 로고
    • A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships
    • Gold ND, Jackson RM (2006) A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships. J Chem Inf Model 46: 736-742.
    • (2006) J Chem Inf Model , vol.46 , pp. 736-742
    • Gold, N.D.1    Jackson, R.M.2
  • 87
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • DOI 10.1016/S0022-2836(02)00811-2
    • Schmitt S, Kuhn D, Klebe G (2003) A new method to detect related function among proteins independent of sequence and fold homology. J Mol Biol 323: 387-406. (Pubitemid 35283699)
    • (2002) Journal of Molecular Biology , vol.323 , Issue.2 , pp. 387-406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.3
  • 88
    • 33744935012 scopus 로고    scopus 로고
    • From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase
    • DOI 10.1016/j.jmb.2006.04.024, PII S0022283606004724
    • Kuhn D, Weskamp N, Schmitt S, Hullermeier E, Klebe G (2006) From the similarity analysis of protein cavities to the functional classification of protein families using cavbase. J Mol Biol 359: 1023-1044. (Pubitemid 43842050)
    • (2006) Journal of Molecular Biology , vol.359 , Issue.4 , pp. 1023-1044
    • Kuhn, D.1    Weskamp, N.2    Schmitt, S.3    Hullermeier, E.4    Klebe, G.5
  • 89
    • 3543053391 scopus 로고    scopus 로고
    • Efficient similarity search in protein structure databases by k-clique hashing
    • DOI 10.1093/bioinformatics/bth113
    • Weskamp N, Kuhn D, Hullermeier E, Klebe G (2004) Efficient similarity search in protein structure databases by k-clique hashing. Bioinformatics 20: 1522-1526. (Pubitemid 39023156)
    • (2004) Bioinformatics , vol.20 , Issue.10 , pp. 1522-1526
    • Weskamp, N.1    Kuhn, D.2    Hullermeier, E.3    Klebe, G.4
  • 91
    • 3242890667 scopus 로고    scopus 로고
    • PDBSiteScan: A program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins
    • DOI 10.1093/nar/gkh439
    • Ivanisenko VA, Pintus SS, Grigorovich DA, Kolchanov NA (2004) PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res 32: W549-W554. (Pubitemid 38997394)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS
    • Ivanisenko, V.A.1    Pintus, S.S.2    Grigorovich, D.A.3    Kolchanov, N.A.4
  • 92
    • 0036288284 scopus 로고    scopus 로고
    • Identification of protein functions from a molecular surface database, eF-site
    • Kinoshita K, Furui J, Nakamura H (2001) Identification of protein functions from a molecular surface database, eF-site. J Struct Funct Genomics 2: 9-22.
    • (2001) J Struct Funct Genomics , vol.2 , pp. 9-22
    • Kinoshita, K.1    Furui, J.2    Nakamura, H.3
  • 93
    • 0041842509 scopus 로고    scopus 로고
    • Identification of protein biochemical functions by similarity search using the molecular surface database eF-site
    • DOI 10.1110/ps.0368703
    • Kinoshita K, Nakamura H (2003) Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sci 12: 1589-1595. (Pubitemid 36910039)
    • (2003) Protein Science , vol.12 , Issue.8 , pp. 1589-1595
    • Kinoshita, K.1    Nakamura, H.2
  • 94
    • 3242883091 scopus 로고    scopus 로고
    • PvSOAR: Detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins
    • DOI 10.1093/nar/gkh390
    • Binkowski TA, Freeman P, Liang J (2004) pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins. Nucleic Acids Res 32: W555-W558. (Pubitemid 38997395)
    • (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS
    • Binkowski, T.A.1    Freeman, P.2    Liang, J.3
  • 95
    • 61649106689 scopus 로고    scopus 로고
    • Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns
    • Tseng YY, Dundas J, Liang J (2009) Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns. J Mol Biol 387: 451-464.
    • (2009) J Mol Biol , vol.387 , pp. 451-464
    • Tseng, Y.Y.1    Dundas, J.2    Liang, J.3
  • 96
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147: 195-197.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 97
    • 0042890523 scopus 로고    scopus 로고
    • Inferring functional relationships of proteins from local sequence and spatial surface patterns
    • DOI 10.1016/S0022-2836(03)00882-9
    • Binkowski TA, Adamian L, Liang J (2003) Inferring functional relationships of proteins from local sequence and spatial surface patterns. J Mol Biol 332: 505-526. (Pubitemid 37013514)
    • (2003) Journal of Molecular Biology , vol.332 , Issue.2 , pp. 505-526
    • Binkowski, T.A.1    Adamian, L.2    Liang, J.3
  • 98
    • 22544486576 scopus 로고    scopus 로고
    • Protein function prediction using local 3D templates
    • DOI 10.1016/j.jmb.2005.05.067, PII S0022283605006340
    • Laskowski RA, Watson JD, Thornton JM (2005) Protein function prediction using local 3D templates. J Mol Biol 351: 614-626. (Pubitemid 41021944)
    • (2005) Journal of Molecular Biology , vol.351 , Issue.3 , pp. 614-626
    • Laskowski, R.A.1    Watson, J.D.2    Thornton, J.M.3
  • 99
    • 20444450051 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structural data
    • DOI 10.1016/j.sbi.2005.04.003, PII S0959440X05000825
    • Watson JD, Laskowski RA, Thornton JM (2005) Predicting protein function from sequence and structural data. Curr Opin Struct Biol 15: 275-284. (Pubitemid 40826446)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.3 SPEC. ISS , pp. 275-284
    • Watson, J.D.1    Laskowski, R.A.2    Thornton, J.M.3
  • 100
    • 33748257987 scopus 로고    scopus 로고
    • A virtual active compound produced from the negative image of a ligand-binding pocket, and its application to in-silico drug screening
    • DOI 10.1007/s10822-006-9047-1
    • Fukunishi Y, Kubota S, Kanai C, Nakamura H (2006) A virtual active compound produced from the negative image of a ligand-binding pocket, and its application to in-silico drug screening. J Comput Aided Mol Des 20: 237-248. (Pubitemid 44317516)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.4 , pp. 237-248
    • Fukunishi, Y.1    Kubota, S.2    Kanai, C.3    Nakamura, H.4
  • 101
    • 48749125396 scopus 로고    scopus 로고
    • Pseudoreceptor models in drug design: Bridging ligand- and receptor-based virtual screening
    • Tanrikulu Y, Schneider G (2008) Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening. Nat Rev Drug Discov 7: 667-677.
    • (2008) Nat Rev Drug Discov , vol.7 , pp. 667-677
    • Tanrikulu, Y.1    Schneider, G.2
  • 102
    • 11244335640 scopus 로고    scopus 로고
    • Strategies for multiple signalling inhibition
    • Tortora G, Bianco R, Daniele G (2004) Strategies for multiple signalling inhibition. J Chemother 16 (Suppl 4): 41-43. (Pubitemid 40065279)
    • (2004) Journal of Chemotherapy , vol.16 , Issue.SUPPL. 4 , pp. 41-43
    • Tortora, G.1    Bianco, R.2    Daniele, G.3
  • 103
    • 66349119013 scopus 로고    scopus 로고
    • A unified statistical model to support local sequence order independent similarity searching for ligand binding sites and its application to genome-based drug discovery
    • In press
    • Xie L, Xie L, Bourne PE (2009) A unified statistical model to support local sequence order independent similarity searching for ligand binding sites and its application to genome-based drug discovery. Bioinformatics; In press.
    • (2009) Bioinformatics
    • Xie, L.1    Xie, L.2    Bourne, P.E.3
  • 104
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 9: 739-747. (Pubitemid 28434482)
    • (1998) Protein Engineering , vol.11 , Issue.9 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 105
    • 33747818007 scopus 로고    scopus 로고
    • CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
    • DOI 10.1093/nar/gkl282
    • Dundas J, Zheng O, Tseng J, Binkowski B, Turpaz Y, et al. (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated resiudes. Nucleic Acids Res 34: W116-W118. (Pubitemid 44529746)
    • (2006) Nucleic Acids Research , vol.34 , Issue.WEB. SERV. ISS
    • Dundas, J.1    Ouyang, Z.2    Tseng, J.3    Binkowski, A.4    Turpaz, Y.5    Liang, J.6
  • 106
    • 13844312649 scopus 로고    scopus 로고
    • ZINC - A free database of commercially available compounds for virtual screening
    • Shoichet BK, Irwin JJ (2005) ZINC - a free database of commercially available compounds for virtual screening. J Chem Inf Model 45: 177-182.
    • (2005) J Chem Inf Model , vol.45 , pp. 177-182
    • Shoichet, B.K.1    Irwin, J.J.2


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