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Volumn 10, Issue 7, 2005, Pages 667-674

Here be dragons: Docking and screening in an uncharted region of chemical space

Author keywords

Database preparation; High throughput screening; HTS; Molecular docking; Virtual screening

Indexed keywords

ASPARTIC ACID; DIHYDROFOLATE REDUCTASE; DIHYDROFOLATE REDUCTASE INHIBITOR; FOLIC ACID; LIGAND; METHOTREXATE;

EID: 23844456151     PISSN: 10870571     EISSN: 1552454X     Source Type: Journal    
DOI: 10.1177/1087057105281047     Document Type: Article
Times cited : (39)

References (31)
  • 1
    • 0037235881 scopus 로고    scopus 로고
    • Virtual screening to enrich hit lists from high-throughput screening: A case study on small-molecule inhibitors of angiogenin
    • Jenkins JL, Kao RY, Shapiro R: Virtual screening to enrich hit lists from high-throughput screening: a case study on small-molecule inhibitors of angiogenin. Proteins 2003;50:81-93.
    • (2003) Proteins , vol.50 , pp. 81-93
    • Jenkins, J.L.1    Kao, R.Y.2    Shapiro, R.3
  • 2
    • 0037161605 scopus 로고    scopus 로고
    • Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B
    • Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, et al: Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem 2002;45:2213-2221.
    • (2002) J Med Chem , vol.45 , pp. 2213-2221
    • Doman, T.N.1    McGovern, S.L.2    Witherbee, B.J.3    Kasten, T.P.4    Kurumbail, R.5    Stallings, W.C.6
  • 5
    • 26944457287 scopus 로고    scopus 로고
    • Experimental screening of dihydrofolate reductase yields a "test set" of 50,000 small molecules for a computational data-mining and docking competition
    • Elowe NH, Blanchard JE, Cechetto JD, Brown ED: Experimental screening of dihydrofolate reductase yields a "test set" of 50,000 small molecules for a computational data-mining and docking competition. J Biomol Screen 2005;10:653-657.
    • (2005) J Biomol Screen , vol.10 , pp. 653-657
    • Elowe, N.H.1    Blanchard, J.E.2    Cechetto, J.D.3    Brown, E.D.4
  • 6
    • 0038309300 scopus 로고    scopus 로고
    • High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate
    • Zolli-Juran M, Cechetto JD, Hartlen R, Daigle DM, Brown ED: High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. Bioorg Med Chem Lett 2003;13:2493-2496.
    • (2003) Bioorg Med Chem Lett , vol.13 , pp. 2493-2496
    • Zolli-Juran, M.1    Cechetto, J.D.2    Hartlen, R.3    Daigle, D.M.4    Brown, E.D.5
  • 7
    • 13844312649 scopus 로고    scopus 로고
    • ZINC-a free database of commercially available compounds for virtual screening
    • Irwin JJ, Shoichet BK: ZINC-a free database of commercially available compounds for virtual screening. J Chem Inf Model 2005;45:177-182.
    • (2005) J Chem Inf Model , vol.45 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 9
    • 84986432941 scopus 로고
    • Automated docking with grid-based energy evaluation
    • Meng EC, Shoichet B, Kuntz ID: Automated docking with grid-based energy evaluation. J Comp Chem 1992;13:505-524.
    • (1992) J Comp Chem , vol.13 , pp. 505-524
    • Meng, E.C.1    Shoichet, B.2    Kuntz, I.D.3
  • 11
    • 0031965676 scopus 로고    scopus 로고
    • Flexible ligand docking using conformational ensembles
    • Lorber DM, Shoichet BK: Flexible ligand docking using conformational ensembles. Protein Sci 1998;7:938-950.
    • (1998) Protein Sci , vol.7 , pp. 938-950
    • Lorber, D.M.1    Shoichet, B.K.2
  • 12
    • 0036108486 scopus 로고    scopus 로고
    • Protein-protein docking with multiple residue conformations and residue substitutions
    • Lorber DM, Udo MK, Shoichet BK: Protein-protein docking with multiple residue conformations and residue substitutions. Protein Sci 2002;11:1393-1408.
    • (2002) Protein Sci , vol.11 , pp. 1393-1408
    • Lorber, D.M.1    Udo, M.K.2    Shoichet, B.K.3
  • 13
    • 0031015737 scopus 로고    scopus 로고
    • Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence
    • Sawaya MR, Kraut J: Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Biochemistry 1997;36:586-603.
    • (1997) Biochemistry , vol.36 , pp. 586-603
    • Sawaya, M.R.1    Kraut, J.2
  • 14
    • 0037436339 scopus 로고    scopus 로고
    • Relibase: Design and development of a database for comprehensive analysis of protein-ligand interactions
    • Hendlich M, Bergner A, Gunther J, Klebe G: Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. J Mol Biol 2003;326:607-620.
    • (2003) J Mol Biol , vol.326 , pp. 607-620
    • Hendlich, M.1    Bergner, A.2    Gunther, J.3    Klebe, G.4
  • 15
    • 0035974647 scopus 로고    scopus 로고
    • X-ray crystal structures of Candida albicans dihydrofolate reductase: High resolution ternary complexes in which the dihydronicotinamide moiety of NADPH is displaced by an inhibitor
    • Whitlow M, Howard AJ, Stewart D, Hardman KD, Chan JH, Baccanari DP, et al: X-ray crystal structures of Candida albicans dihydrofolate reductase: high resolution ternary complexes in which the dihydronicotinamide moiety of NADPH is displaced by an inhibitor. J Med Chem 2001;44:2928-2932.
    • (2001) J Med Chem , vol.44 , pp. 2928-2932
    • Whitlow, M.1    Howard, A.J.2    Stewart, D.3    Hardman, K.D.4    Chan, J.H.5    Baccanari, D.P.6
  • 16
    • 0029315603 scopus 로고
    • MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry
    • Gerber P, Müller K: MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry. J Comput Aided Mol Des 1995;9:251-268.
    • (1995) J Comput Aided Mol des , vol.9 , pp. 251-268
    • Gerber, P.1    Müller, K.2
  • 17
    • 0036076470 scopus 로고    scopus 로고
    • Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase
    • Powers RA, Morandi F, Shoichet BK: Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase. Structure (Camb) 2002;10:1013-1023.
    • (2002) Structure (Camb) , vol.10 , pp. 1013-1023
    • Powers, R.A.1    Morandi, F.2    Shoichet, B.K.3
  • 18
    • 4744365803 scopus 로고    scopus 로고
    • Soft docking and multiple receptor conformations in virtual screening
    • Ferrari AM, Wei BQ, Costantino L, Shoichet BK: Soft docking and multiple receptor conformations in virtual screening. J Med Chem 2004;47:5076-5084.
    • (2004) J Med Chem , vol.47 , pp. 5076-5084
    • Ferrari, A.M.1    Wei, B.Q.2    Costantino, L.3    Shoichet, B.K.4
  • 19
    • 0038460858 scopus 로고    scopus 로고
    • Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
    • McGovern SL, Shoichet BK: Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem 2003;46:2895-2907.
    • (2003) J Med Chem , vol.46 , pp. 2895-2907
    • McGovern, S.L.1    Shoichet, B.K.2
  • 21
    • 84986518987 scopus 로고
    • Molecular docking using shape descriptors
    • Shoichet B, Bodian DL, Kuntz ID: Molecular docking using shape descriptors. J Comp Chem 1992;13:380-397.
    • (1992) J Comp Chem , vol.13 , pp. 380-397
    • Shoichet, B.1    Bodian, D.L.2    Kuntz, I.D.3
  • 22
    • 0023280069 scopus 로고
    • Calculation of electrostatic potentials in an enzyme active site
    • Gilson MK, Honig BH: Calculation of electrostatic potentials in an enzyme active site. Nature 1987;330:84-86.
    • (1987) Nature , vol.330 , pp. 84-86
    • Gilson, M.K.1    Honig, B.H.2
  • 24
    • 0027385177 scopus 로고
    • Matching chemistry and shape in molecular docking
    • Shoichet BK, Kuntz ID: Matching chemistry and shape in molecular docking. Protein Eng 1993;6:723-732.
    • (1993) Protein Eng , vol.6 , pp. 723-732
    • Shoichet, B.K.1    Kuntz, I.D.2
  • 25
    • 0017785773 scopus 로고
    • Dihydrofolate reductase: X-ray structure of the binary complex with methotrexate
    • Matthews DA, Alden RA, Bolin JT, Freer ST, Hamlin R, Xuong N, et al: Dihydrofolate reductase: x-ray structure of the binary complex with methotrexate. Science 1977;197:452-455.
    • (1977) Science , vol.197 , pp. 452-455
    • Matthews, D.A.1    Alden, R.A.2    Bolin, J.T.3    Freer, S.T.4    Hamlin, R.5    Xuong, N.6
  • 26
    • 0342738215 scopus 로고
    • Spectroscopic studies of some Pd(Ii), Pt(Ii), Ag(I), and Au(Iii) complexes of 4,6-diamino-2-thiopyrimidine and 4,6-diamino-2- methylthiopyrimidine-structure and binding-site determination
    • Gutierrez MD, Lopez R, Romero MA, Salas JM: Spectroscopic studies of some Pd(Ii), Pt(Ii), Ag(I), and Au(Iii) complexes of 4,6-diamino-2-thiopyrimidine and 4,6-diamino-2-methylthiopyrimidine-structure and binding-site determination. Can J Chem 1988;66:249-255.
    • (1988) Can J Chem , vol.66 , pp. 249-255
    • Gutierrez, M.D.1    Lopez, R.2    Romero, M.A.3    Salas, J.M.4
  • 27
    • 0036666325 scopus 로고    scopus 로고
    • The ionization constants of 2-substituted 4,6-diamino-s-triazines: The applicability to the Hammett and Taft equations
    • Tashiro T: The ionization constants of 2-substituted 4,6-diamino-s- triazines: the applicability to the Hammett and Taft equations. J Heterocyclic Chem 2002;39:615-622.
    • (2002) J Heterocyclic Chem , vol.39 , pp. 615-622
    • Tashiro, T.1
  • 28
    • 37049144701 scopus 로고
    • Pteridine studies: Part III. The solubility and the stability to hydrolysis of pteridines
    • Albert A, Brown DJ, Cheeseman G: Pteridine studies: part III. The solubility and the stability to hydrolysis of pteridines. J Chem Soc 1952:4219-4232.
    • (1952) J Chem Soc , pp. 4219-4232
    • Albert, A.1    Brown, D.J.2    Cheeseman, G.3
  • 29
    • 0025212168 scopus 로고
    • Studies of thiouracils: 2. Tautomerism and infrared-spectra of thiouracils-matrix-isolation and abinitio studies
    • Rostkowska H, Szczepaniak K, Nowak MJ, Leszczynski J, Kubulat K, Person WB: Studies of thiouracils: 2. Tautomerism and infrared-spectra of thiouracils-matrix-isolation and abinitio studies. J Am Chem Soc 1990;112: 2147-2160.
    • (1990) J Am Chem Soc , vol.112 , pp. 2147-2160
    • Rostkowska, H.1    Szczepaniak, K.2    Nowak, M.J.3    Leszczynski, J.4    Kubulat, K.5    Person, W.B.6
  • 30
    • 0033625045 scopus 로고    scopus 로고
    • Ab initio study on tautomerism of 2-thiouracil in the gas phase and in solution
    • Yekeler H: Ab initio study on tautomerism of 2-thiouracil in the gas phase and in solution. J Comput Aid Mol Des 2000;14:243-250.
    • (2000) J Comput Aid Mol des , vol.14 , pp. 243-250
    • Yekeler, H.1
  • 31
    • 0033668806 scopus 로고    scopus 로고
    • Virtual screening: An alternative or complement to high throughput screening? Preface
    • Klebe G: Virtual screening: an alternative or complement to high throughput screening? Preface. Perspect Drug Discov Des 2000;20:vii-xi.
    • (2000) Perspect Drug Discov des , vol.20
    • Klebe, G.1


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