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Volumn 51, Issue 2, 2003, Pages 172-188

Pharmacophore-based molecular docking to account for ligand flexibility

Author keywords

Database searching; Pharmacophoric ensembles; PhDOCK; Virtual screening

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ARTICLE; DATA BASE; LIGAND BINDING; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; MOLECULE; PHARMACOPHORE; PRIORITY JOURNAL; VALIDATION PROCESS;

EID: 0037402105     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10266     Document Type: Article
Times cited : (91)

References (37)
  • 2
    • 0031181346 scopus 로고    scopus 로고
    • QXP Powerful, rapid computer algorithms for structure-based drug design
    • McMartin C, Bohacek RS. QXP: Powerful, rapid computer algorithms for structure-based drug design. J Comp Aided Mol Design 1997;11:333-344.
    • (1997) J Comp Aided Mol Design , vol.11 , pp. 333-344
    • McMartin, C.1    Bohacek, R.S.2
  • 3
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997;267:727-748.
    • (1997) J Mol Biol , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 4
    • 0029294584 scopus 로고
    • Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
    • Gehlhaar DK, Verkhivker GM, Rejto PA, Sherman CJ, Fogel DB, Fogel LJ, Freer ST. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Chem Biol 1995;2:317-324.
    • (1995) Chem Biol , vol.2 , pp. 317-324
    • Gehlhaar, D.K.1    Verkhivker, G.M.2    Rejto, P.A.3    Sherman, C.J.4    Fogel, D.B.5    Fogel, L.J.6    Freer, S.T.7
  • 6
    • 0030203710 scopus 로고    scopus 로고
    • Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
    • Morris GM, Goodsell DS, Huey R, Olson AJ. Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4. J Comp Aided Mol Design 1996;10:293-304.
    • (1996) J Comp Aided Mol Design , vol.10 , pp. 293-304
    • Morris, G.M.1    Goodsell, D.S.2    Huey, R.3    Olson, A.J.4
  • 7
    • 0031296686 scopus 로고    scopus 로고
    • CASP2 experiences with docking flexible ligands using FLEXX
    • Kramer B, Rarey M, Lengauer T. CASP2 experiences with docking flexible ligands using FLEXX. Proteins 1997;Suppl 1:221-225.
    • (1997) Proteins , pp. 221-225
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 8
    • 0030076041 scopus 로고    scopus 로고
    • Placement of medium-sized molecular fragments into active sites of proteins
    • Rarey M, Wefing S, Lengauer T. Placement of medium-sized molecular fragments into active sites of proteins. J Comp Aided Mol Design 1996;10:41-54.
    • (1996) J Comp Aided Mol Design , vol.10 , pp. 41-54
    • Rarey, M.1    Wefing, S.2    Lengauer, T.3
  • 9
    • 0001139413 scopus 로고    scopus 로고
    • Automated flexible ligand docking method and its application for database search
    • Makino S, Kuntz ID. Automated flexible ligand docking method and its application for database search. J Comput Chem 1997;18: 1812-1825.
    • (1997) J Comput Chem , vol.18 , pp. 1812-1825
    • Makino, S.1    Kuntz, I.D.2
  • 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
  • 13
    • 0035254959 scopus 로고    scopus 로고
    • Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation
    • Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW, Shoichet BK. Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation. Proteins 2001;42:279-293.
    • (2001) Proteins , vol.42 , pp. 279-293
    • Su, A.I.1    Lorber, D.M.2    Weston, G.S.3    Baase, W.A.4    Matthews, B.W.5    Shoichet, B.K.6
  • 14
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • Ewing T, Makino S, Skillman A, Kuntz I. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases. J Comp Aided Mol Design 2001;15:411-428.
    • (2001) J Comp Aided Mol Design , vol.15 , pp. 411-428
    • Ewing, T.1    Makino, S.2    Skillman, A.3    Kuntz, I.4
  • 15
    • 0037402655 scopus 로고    scopus 로고
    • Automated generation of MCSS-derived pharmacophoric DOCK site points for searching multi-conformation databases
    • Joseph-McCarthy D, Thomas BE IV, Alvarez JC. Automated generation of MCSS-derived pharmacophoric DOCK site points for searching multi-conformation databases. Proteins 2003;51:189-202.
    • (2003) Proteins , vol.51 , pp. 189-202
    • Joseph-McCarthy, D.1    Thomas B.E. IV2    Alvarez, J.C.3
  • 17
    • 84986432941 scopus 로고
    • Automated docking with grid-based energy evaluation
    • Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy evaluation. J Comput Chem 1992;13:505-524.
    • (1992) J Comput Chem , vol.13 , pp. 505-524
    • Meng, E.C.1    Shoichet, B.K.2    Kuntz, I.D.3
  • 20
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation energies in molecular systems
    • Neria E, Fischer S, Karplus M. Simulation of activation energies in molecular systems. J Chem Phys 1996;105:1902-1921.
    • (1996) J Chem Phys , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 24
    • 0033153283 scopus 로고    scopus 로고
    • Pro-1 of macrophage migration inhibitory factor functions as a catalytic base in the phenylpyruvate tautomerase activity
    • Lubetsky JB, Swope M, Dealwis C, Blake P, Lolis E. Pro-1 of macrophage migration inhibitory factor functions as a catalytic base in the phenylpyruvate tautomerase activity. Biochemistry 1999;38:7346-7354.
    • (1999) Biochemistry , vol.38 , pp. 7346-7354
    • Lubetsky, J.B.1    Swope, M.2    Dealwis, C.3    Blake, P.4    Lolis, E.5
  • 25
    • 0029863567 scopus 로고    scopus 로고
    • Inhibition and catalytic mechanism of HIV-1 aspartic protease
    • Silva AM, Cachau RE, Sham HL, Erickson JW. Inhibition and catalytic mechanism of HIV-1 aspartic protease. J Mol Biol 1996;255:321-340.
    • (1996) J Mol Biol , vol.255 , pp. 321-340
    • Silva, A.M.1    Cachau, R.E.2    Sham, H.L.3    Erickson, J.W.4
  • 26
    • 0031024171 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 1997;23:3-25.
    • (1997) Adv Drug Deliv Rev , vol.23 , pp. 3-25
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 27
    • 0020441466 scopus 로고
    • Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution. I. General features and binding of methotrexate
    • Bolin JT, Filman DJ, Matthews DA, Hamlin RC, Kraut J. Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution. I. General features and binding of methotrexate. J Biol Chem 1982;257:13650.
    • (1982) J Biol Chem , vol.257 , pp. 13650
    • Bolin, J.T.1    Filman, D.J.2    Matthews, D.A.3    Hamlin, R.C.4    Kraut, J.5
  • 28
    • 0028960221 scopus 로고
    • Role of the active site carboxylate in dihydrofolate reductase: Kinetic and spectroscopic strudies of the aspartate 25 → asparagine mutant of the Lactobacillus casei enzyme
    • Basran J, Casarotto MG, Barsukov IL, Roberts GCK. Role of the active site carboxylate in dihydrofolate reductase: kinetic and spectroscopic strudies of the aspartate 25 → asparagine mutant of the Lactobacillus casei enzyme. Biochemistry 1995;34:2872-2882.
    • (1995) Biochemistry , vol.34 , pp. 2872-2882
    • Basran, J.1    Casarotto, M.G.2    Barsukov, I.L.3    Roberts, G.C.K.4
  • 29
    • 0019781030 scopus 로고
    • Netgative cooperativity between folinic acid and coenzyme in their binding to Lactobacillus casei dihydrofolate reductase
    • Birdsall B, Burgen AS, Hyde EL, Roberts GC, Feeney J. Netgative cooperativity between folinic acid and coenzyme in their binding to Lactobacillus casei dihydrofolate reductase. Biochemistry 1981; 20:7186-7195.
    • (1981) Biochemistry , vol.20 , pp. 7186-7195
    • Birdsall, B.1    Burgen, A.S.2    Hyde, E.L.3    Roberts, G.C.4    Feeney, J.5
  • 30
    • 0029123503 scopus 로고
    • Solution structure of a brodimoprim analogue in its complex with Lactobacillus casei dihydrofolate reductase
    • Morgan WD, Birdsall B, Polshakov VI, Sali D, Kompis I, Feeney J. Solution structure of a brodimoprim analogue in its complex with Lactobacillus casei dihydrofolate reductase. Biochemistry 1995;34: 11690-11702.
    • (1995) Biochemistry , vol.34 , pp. 11690-11702
    • Morgan, W.D.1    Birdsall, B.2    Polshakov, V.I.3    Sali, D.4    Kompis, I.5    Feeney, J.6
  • 32
    • 0021288986 scopus 로고
    • Properties of brodimoprim as an inhibitor of DHFR
    • Then RL, Hermann F. Properties of brodimoprim as an inhibitor of DHFR. Chemotherapy 1984;30:18-25.
    • (1984) Chemotherapy , vol.30 , pp. 18-25
    • Then, R.L.1    Hermann, F.2
  • 33
    • 0028985318 scopus 로고
    • Isomorphous crystal structures of Escherichia coli dihydrofolate reductase complexed with folate, 5-deazafolate, and 5, 10-dideazatetrahydrofolate: Mechanistic implications
    • Reyes VM, Sawaya MR, Brown KA, Kraut J. Isomorphous crystal structures of Escherichia coli dihydrofolate reductase complexed with folate, 5-deazafolate, and 5, 10-dideazatetrahydrofolate: mechanistic implications. Biochemistry 1995;34:2710-2723.
    • (1995) Biochemistry , vol.34 , pp. 2710-2723
    • Reyes, V.M.1    Sawaya, M.R.2    Brown, K.A.3    Kraut, J.4
  • 34
  • 35
    • 0029990447 scopus 로고    scopus 로고
    • 2,4-Diamino-5-deaza-6-substituted pyrido[2,3-d]pyrimidine antifolates as potent and selective non-classical inhibitors of dihydrofolate reductases
    • Gangjee A, Vidwans AP, Queener SF, Kisliuk RL. 2,4-Diamino-5-deaza-6-substituted pyrido[2,3-d]pyrimidine antifolates as potent and selective non-classical inhibitors of dihydrofolate reductases. J Med Chem 1996;39:1438-1446.
    • (1996) J Med Chem , vol.39 , pp. 1438-1446
    • Gangjee, A.1    Vidwans, A.P.2    Queener, S.F.3    Kisliuk, R.L.4
  • 36
    • 0035438391 scopus 로고    scopus 로고
    • Is there a difference between leads and drugs? A historical perspective
    • Oprea TI, Davis AM, Teague SJ, Leeson PD. Is there a difference between leads and drugs? A historical perspective. J Chem Inf Comput Sci 2001;41:1308-1315.
    • (2001) J Chem Inf Comput Sci , vol.41 , pp. 1308-1315
    • Oprea, T.I.1    Davis, A.M.2    Teague, S.J.3    Leeson, P.D.4
  • 37
    • 0005123846 scopus 로고
    • Automated chemical hypothesis generation and database searching with Catalyst(R)
    • Sprague PW. Automated chemical hypothesis generation and database searching with Catalyst(R). Perspect Drug Disc Design 1995;3:1-20.
    • (1995) Perspect Drug Disc Design , vol.3 , pp. 1-20
    • Sprague, P.W.1


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