메뉴 건너뛰기




Volumn 1076, Issue , 2011, Pages 71-88

A computational fragment approach by mining the protein data bank: Library design and bioisosterism

Author keywords

[No Author keywords available]

Indexed keywords

DRUG DELIVERY; LIGANDS; PROTEINS;

EID: 84905575615     PISSN: 00976156     EISSN: 19475918     Source Type: Book Series    
DOI: 10.1021/bk-2011-1076.ch005     Document Type: Conference Paper
Times cited : (3)

References (29)
  • 2
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • Schmitt, S.; Kuhn, D.; Klebe, G. A new method to detect related function among proteins independent of sequence and fold homology. J. Mol. Biol. 2000, 323, 387-406.
    • (2000) J. Mol. Biol. , vol.323 , pp. 387-406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.3
  • 3
    • 0037661398 scopus 로고    scopus 로고
    • A new bioinformatic approach to detect common 3D sites in protein structures
    • Jambon, M.; Imberty, A.; Deleage, G.; Geourjon, C A new bioinformatic approach to detect common 3D sites in protein structures. Proteins 2003, 52, 137-145.
    • (2003) Proteins , vol.52 , pp. 137-145
    • Jambon, M.1    Imberty, A.2    Deleage, G.3    Geourjon, C.4
  • 4
    • 2442614144 scopus 로고    scopus 로고
    • Recognition of functional sites in protein structures
    • Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J. Recognition of functional sites in protein structures. J. Mol. Biol. 2004, 339, 607-633.
    • (2004) J. Mol. Biol. , vol.339 , pp. 607-633
    • Shulman-Peleg, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 5
    • 33644876699 scopus 로고    scopus 로고
    • SitesBase: A database for structure-based protein-ligand binding site comparisons
    • Gold, N. D.; Jackson, R. M. SitesBase: A database for structure-based protein-ligand binding site comparisons. Nucleic Acids Res. 2006, 34, D231-234.
    • (2006) Nucleic Acids Res. , vol.34
    • Gold, N.D.1    Jackson, R.M.2
  • 6
    • 33748449489 scopus 로고    scopus 로고
    • STRUCTFAST: Protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring
    • Debe, D. A.; Danzer, J. F.; Goddard, W. A.; Poleksic, A. STRUCTFAST: Protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring. Proteins 2006, 64 (4), 960-7.
    • (2006) Proteins , vol.64 , Issue.4 , pp. 960-967
    • Debe, D.A.1    Danzer, J.F.2    Goddard, W.A.3    Poleksic, A.4
  • 7
    • 34548778124 scopus 로고    scopus 로고
    • A novel approach to local similarity of protein binding sites substantially improves computational drug design results
    • Ramensky, V.; Sobol, A.; Zaitseva, N.; Rubinov, A.; Zosimov, V. A novel approach to local similarity of protein binding sites substantially improves computational drug design results. Proteins 2007, 69, 349-57.
    • (2007) Proteins , vol.69 , pp. 349-357
    • Ramensky, V.1    Sobol, A.2    Zaitseva, N.3    Rubinov, A.4    Zosimov, V.5
  • 8
    • 44349119204 scopus 로고    scopus 로고
    • A simple and fuzzy method to align and compare druggable ligand-binding sites
    • Jun
    • Schalon, C.; Surgand, J.-S.; Kellenberger, E.; Rognan, D. A simple and fuzzy method to align and compare druggable ligand-binding sites. Proteins 2008Jun, 71 (4), 1755-78.
    • (2008) Proteins , vol.71 , Issue.4 , pp. 1755-1778
    • Schalon, C.1    Surgand, J.-S.2    Kellenberger, E.3    Rognan, D.4
  • 9
    • 61449104961 scopus 로고    scopus 로고
    • Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques
    • Brenke, R.; Kozakov, D.; Chuang, G. Y.; Beglov, D.; Hall, D.; Landon, M. R.; Mattos, C.; Vajda, S. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics 2009, 25 (5), 621-7.
    • (2009) Bioinformatics , vol.25 , Issue.5 , pp. 621-627
    • Brenke, R.1    Kozakov, D.2    Chuang, G.Y.3    Beglov, D.4    Hall, D.5    Landon, M.R.6    Mattos, C.7    Vajda, S.8
  • 10
    • 77956040809 scopus 로고    scopus 로고
    • Pocket similarity: Are alpha carbons enough?
    • Feldman, H. J.; Labute, P. Pocket similarity: are alpha carbons enough? J. Chem. Inf. Model. 2010, 50 (8), 1466-75.
    • (2010) J. Chem. Inf. Model. , vol.50 , Issue.8 , pp. 1466-1475
    • Feldman, H.J.1    Labute, P.2
  • 11
    • 65249163786 scopus 로고    scopus 로고
    • Functional annotation strategy for protein structures
    • Doppelt, O.; Moriaud, F.; Bornot, A.; de Brevern, A. G. Functional annotation strategy for protein structures. Bioinformation 2007, 1 (9), 357-9.
    • (2007) Bioinformation , vol.1 , Issue.9 , pp. 357-359
    • Doppelt, O.1    Moriaud, F.2    Bornot, A.3    De Brevern, A.G.4
  • 13
    • 77950284284 scopus 로고    scopus 로고
    • Fast and automated functional classification with MED-SuMo: An application on purine-binding proteins
    • Doppelt-Azeroual, O.; Delfaud, F.; Moriaud, F.; de Brevern, A. G. Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. Protein Sci. 2010, 19 (4), 847-67.
    • (2010) Protein Sci. , vol.19 , Issue.4 , pp. 847-867
    • Doppelt-Azeroual, O.1    Delfaud, F.2    Moriaud, F.3    De Brevern, A.G.4
  • 17
    • 2442647742 scopus 로고    scopus 로고
    • BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, p38, and HIV protease
    • Pierce, A. C.; Rao, G.; Bemis, G. W. BREED: Generating novel inhibitors through hybridization of known ligands. Application to CDK2, p38, and HIV protease. J. Med. Chem. 2004, 47, 2768-75.
    • (2004) J. Med. Chem. , vol.47 , pp. 2768-2775
    • Pierce, A.C.1    Rao, G.2    Bemis, G.W.3
  • 18
    • 33750836761 scopus 로고    scopus 로고
    • Identification of targetspecific bioisosteric fragments from ligand-protein crystallographic data
    • Kennewell, E. A.; Willett, P.; Ducrot, P.; Luttmann, C. Identification of targetspecific bioisosteric fragments from ligand-protein crystallographic data. J. Comput.-Aided Mol. Des. 2006, 20 (6), 385-94.
    • (2006) J. Comput.-Aided Mol. Des. , vol.20 , Issue.6 , pp. 385-394
    • Kennewell, E.A.1    Willett, P.2    Ducrot, P.3    Luttmann, C.4
  • 19
    • 77952732009 scopus 로고    scopus 로고
    • Bioisosteric replacement and scaffold hopping in lead generation and optimization
    • Langdon, S. R.; Ertl, P.; Brown, N. Bioisosteric replacement and scaffold hopping in lead generation and optimization. Mol. Inf. 2010, 29 (5).
    • (2010) Mol. Inf. , vol.29 , Issue.5
    • Langdon, S.R.1    Ertl, P.2    Brown, N.3
  • 20
    • 79955419410 scopus 로고    scopus 로고
    • Synopsis of some recent tactical application of bioisosteres in drug design
    • Meanwell, N. A. Synopsis of some recent tactical application of bioisosteres in drug design. J. Med. Chem. 2011, 54 (8), 2529-91.
    • (2011) J. Med. Chem. , vol.54 , Issue.8 , pp. 2529-2591
    • Meanwell, N.A.1
  • 22
    • 0002404088 scopus 로고
    • On the orthogonal transformation used for structural comparisons
    • Kearsley, S. K. On the orthogonal transformation used for structural comparisons. Acta Crystallogr., Sect. A 1989, 45, 208-210.
    • (1989) Acta Crystallogr., Sect. A , vol.45 , pp. 208-210
    • Kearsley, S.K.1
  • 23
    • 60549090996 scopus 로고    scopus 로고
    • Synthesis of alkenyldiarylmethanes (ADAMs) containing benzo[d]isoxazole and oxazolidin-2-one rings, a new series of potent non-nucleoside HIV-1 reverse transcriptase inhibitors
    • Mar
    • Deng, B. L.; Zhao, Y.; Hartman, T. L.; Watson, K.; Buckheit, R. W., Jr.; Pannecouque, C.; De Clercq, E.; Cushman, M. Synthesis of alkenyldiarylmethanes (ADAMs) containing benzo[d]isoxazole and oxazolidin-2-one rings, a new series of potent non-nucleoside HIV-1 reverse transcriptase inhibitors. Eur. J. Med. Chem. 2009Mar, 44 (3), 1210-4.
    • (2009) Eur. J. Med. Chem. , vol.44 , Issue.3 , pp. 1210-1214
    • Deng, B.L.1    Zhao, Y.2    Hartman, T.L.3    Watson, K.4    Buckheit Jr., R.W.5    Pannecouque, C.6    De Clercq, E.7    Cushman, M.8
  • 24
    • 33846108633 scopus 로고    scopus 로고
    • BindingDB: A web-accessible database of experimentally determined protein-ligand binding affinities
    • Liu, T.; Lin, Y.; Wen, X.; Jorrisen, R. N.; Gilson, M. K. BindingDB: A web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 2007, 35, D198-D201.
    • (2007) Nucleic Acids Res. , vol.35
    • Liu, T.1    Lin, Y.2    Wen, X.3    Jorrisen, R.N.4    Gilson, M.K.5
  • 25
    • 67349154388 scopus 로고    scopus 로고
    • Different poses for ligand and chaperone in inhibitor-bound Hsp90 and GRP94: Implications for paralog-specific drug design
    • Immormino, R. M.; Metzger, L. E.; Reardon, P. N.; Dollins, D. E.; Blagg, B. S.; Gewirth, D. T. Different poses for ligand and chaperone in inhibitor-bound Hsp90 and GRP94: Implications for paralog-specific drug design. J. Mol. Biol. 2009, 388, 1033-1042.
    • (2009) J. Mol. Biol. , vol.388 , pp. 1033-1042
    • Immormino, R.M.1    Metzger, L.E.2    Reardon, P.N.3    Dollins, D.E.4    Blagg, B.S.5    Gewirth, D.T.6
  • 26
    • 0033985080 scopus 로고    scopus 로고
    • GHKL, an emergent ATPase/kinase superfamily
    • Dutta, R.; Inouye, M. GHKL, an emergent ATPase/kinase superfamily. Trends Biochem. Sci. 2000, 25 (1), 24-28.
    • (2000) Trends Biochem. Sci. , vol.25 , Issue.1 , pp. 24-28
    • Dutta, R.1    Inouye, M.2
  • 28
    • 84905561271 scopus 로고    scopus 로고
    • The PubChem Project. http://pubchem.ncbi.nlm.nih.gov.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.