메뉴 건너뛰기




Volumn 4, Issue 3, 2000, Pages 283-286

Structure-based library design: Molecular modelling merges with combinatorial chemistry

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND;

EID: 0038259177     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(00)00090-9     Document Type: Review
Times cited : (68)

References (49)
  • 1
    • 0002716826 scopus 로고    scopus 로고
    • Structure-based design of enzyme inhibitors and receptor ligands
    • Kubinyi H. Structure-based design of enzyme inhibitors and receptor ligands. Curr Opin Drug Disc Dev. 1:1998;4-15.
    • (1998) Curr Opin Drug Disc Dev , vol.1 , pp. 4-15
    • Kubinyi, H.1
  • 2
    • 0031189711 scopus 로고    scopus 로고
    • Molecular recognition of protein-ligand complexes: Applications to drug design
    • Babine R.E., Bender S.L. Molecular recognition of protein-ligand complexes: applications to drug design. Chem Rev. 97:1997;1359-1472.
    • (1997) Chem Rev , vol.97 , pp. 1359-1472
    • Babine, R.E.1    Bender, S.L.2
  • 3
    • 0030712269 scopus 로고    scopus 로고
    • Can drugs be designed?
    • Hubbard R.E. Can drugs be designed? Curr Opin Biotechnol. 8:1997;696-700.
    • (1997) Curr Opin Biotechnol , vol.8 , pp. 696-700
    • Hubbard, R.E.1
  • 4
    • 0030039619 scopus 로고    scopus 로고
    • The art and practice of structure-based drug design: A molecular modeling perspective
    • Bohacek R.S., McMartin C., Guida W.C. The art and practice of structure-based drug design: a molecular modeling perspective. Med Res Rev. 16:1996;3-50.
    • (1996) Med Res Rev , vol.16 , pp. 3-50
    • Bohacek, R.S.1    McMartin, C.2    Guida, W.C.3
  • 6
    • 0010562535 scopus 로고    scopus 로고
    • Applying informatics systems to high-throughput screening and analysis
    • Gund P., Sigal N.H. Applying informatics systems to high-throughput screening and analysis. PharmaInformatics. 1999;S25-S29.
    • (1999) PharmaInformatics
    • Gund, P.1    Sigal, N.H.2
  • 7
    • 0032401982 scopus 로고    scopus 로고
    • High-throughput screening of historic collections: Observations on file size, biological targets and file diversity
    • Spencer R.W. High-throughput screening of historic collections: observations on file size, biological targets and file diversity. Biotechnol Bioeng. 61:1998;61-67.
    • (1998) Biotechnol Bioeng , vol.61 , pp. 61-67
    • Spencer, R.W.1
  • 8
    • 77956764741 scopus 로고    scopus 로고
    • Current and future trends in high throughput screening for drug discovery
    • Oldenburg K.R. Current and future trends in high throughput screening for drug discovery. Annu Rep Med Chem. 33:1998;301-311.
    • (1998) Annu Rep Med Chem , vol.33 , pp. 301-311
    • Oldenburg, K.R.1
  • 9
    • 0040541621 scopus 로고    scopus 로고
    • Combinatorial docking and combinatorial chemistry: Design of potent non-peptide thrombin inhibitors
    • Böhm H.J., Banner D.W., Weber L. Combinatorial docking and combinatorial chemistry: design of potent non-peptide thrombin inhibitors. J Comput Aided Mol Des. 13:1999;51-56.
    • (1999) J Comput Aided Mol des , vol.13 , pp. 51-56
    • Böhm, H.J.1    Banner, D.W.2    Weber, L.3
  • 10
    • 0032196541 scopus 로고    scopus 로고
    • CombiDOCK: Structure-based combinatorial docking and library design
    • Sun Y., Ewing T.J.A., Skillman A.G., Kuntz I.D. CombiDOCK: structure-based combinatorial docking and library design. J Comput Aided Mol Des. 12:1998;579-604.
    • (1998) J Comput Aided Mol des , vol.12 , pp. 579-604
    • Sun, Y.1    Ewing, T.J.A.2    Skillman, A.G.3    Kuntz, I.D.4
  • 13
    • 0031307203 scopus 로고    scopus 로고
    • Evaluation of CASP2 docking section
    • Dixon S.J. Evaluation of CASP2 docking section. Proteins. S1:1997;198-204.
    • (1997) Proteins , vol.1 , pp. 198-204
    • Dixon, S.J.1
  • 14
    • 0032738842 scopus 로고    scopus 로고
    • Evaluation of the FlexX incremental construction algorithm for protein-ligand docking
    • Kramer B., Rarey M., Lengauer T. Evaluation of the FlexX incremental construction algorithm for protein-ligand docking. Proteins. 37:1999;228-241.
    • (1999) Proteins , vol.37 , pp. 228-241
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 15
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones G., Willet P., Glen R.C., Leach A.R., Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol. 267:1997;727-748.
    • (1997) J Mol Biol , vol.267 , pp. 727-748
    • Jones, G.1    Willet, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 16
    • 0031080551 scopus 로고    scopus 로고
    • A new class of models for computing receptor-ligand binding affinities
    • Gilson M.K., Given J.A., Head M.S. A new class of models for computing receptor-ligand binding affinities. Chem Biol. 4:1997;87-92.
    • (1997) Chem Biol , vol.4 , pp. 87-92
    • Gilson, M.K.1    Given, J.A.2    Head, M.S.3
  • 17
    • 0001872472 scopus 로고    scopus 로고
    • Predicting ligand-binding energies
    • Hirst J.D. Predicting ligand-binding energies. Curr Opin Drug Disc Dev. 1:1998;28-33.
    • (1998) Curr Opin Drug Disc Dev , vol.1 , pp. 28-33
    • Hirst, J.D.1
  • 18
    • 0032993815 scopus 로고    scopus 로고
    • Scoring functions: A view from the bench
    • A careful and clear analysis of the shortcomings of current scoring functions
    • Tame J.R.H. Scoring functions: a view from the bench. J Comput Aided Mol Des. 13:1999;99-108. A careful and clear analysis of the shortcomings of current scoring functions.
    • (1999) J Comput Aided Mol des , vol.13 , pp. 99-108
    • Tame, J.R.H.1
  • 21
    • 0032806924 scopus 로고    scopus 로고
    • Relating structure to thermodynamics: The crystal structures and binding affinity of eight OppA-peptide complexes
    • Davies T.G., Hubbard R.E., Tame J.R.H. Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes. Protein Sci. 8:1999;1432-1444.
    • (1999) Protein Sci , vol.8 , pp. 1432-1444
    • Davies, T.G.1    Hubbard, R.E.2    Tame, J.R.H.3
  • 22
    • 0033045557 scopus 로고    scopus 로고
    • Comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors
    • So S.S., Karplus M.A. Comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors. J Comput Aided Mol Des. 13:1999;243-258.
    • (1999) J Comput Aided Mol des , vol.13 , pp. 243-258
    • So, S.S.1    Karplus, M.A.2
  • 23
    • 0032939345 scopus 로고    scopus 로고
    • Ligand solvation in molecular docking
    • Highlights problems that can occur when standard force fields are used as scoring functions and points to a possible solution
    • Shoichet B.K., Leach A.R., Kuntz I.D. Ligand solvation in molecular docking. Proteins. 34:1999;4-16. Highlights problems that can occur when standard force fields are used as scoring functions and points to a possible solution.
    • (1999) Proteins , vol.34 , pp. 4-16
    • Shoichet, B.K.1    Leach, A.R.2    Kuntz, I.D.3
  • 25
    • 0032153192 scopus 로고    scopus 로고
    • Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the method
    • Murray C.W., Auton T.R., Elridge M.D. Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the method. J Comput Aided Mol Des. 12:1999;503-519.
    • (1999) J Comput Aided Mol des , vol.12 , pp. 503-519
    • Murray, C.W.1    Auton, T.R.2    Elridge, M.D.3
  • 26
    • 0001704085 scopus 로고    scopus 로고
    • SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex
    • Wang R., Liu L., Lai L., Tang Y. SCORE: a new empirical method for estimating the binding affinity of a protein-ligand complex. J Mol Model. 4:1998;379-394.
    • (1998) J Mol Model , vol.4 , pp. 379-394
    • Wang, R.1    Liu, L.2    Lai, L.3    Tang, Y.4
  • 27
    • 0032112137 scopus 로고    scopus 로고
    • Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
    • Böhm H.J. Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J Comput Aided Mol Des. 12:1998;309-323.
    • (1998) J Comput Aided Mol des , vol.12 , pp. 309-323
    • Böhm, H.J.1
  • 28
    • 0029294584 scopus 로고
    • Molecular recognition of the inhibitor AG- By HIV-1 protease-conformationally flexible docking by evolutionary programming
    • 317-324
    • Gehlhaar D.K., Verkhivker G.M., Rejto P.A., Sherman C.J., Fogel D.B., Freer S.T. Molecular recognition of the inhibitor AG- by HIV-1 protease-conformationally flexible docking by evolutionary programming. Chem Biol. 1343:1995;2. 317-324.
    • (1995) Chem Biol , vol.1343 , pp. 2
    • Gehlhaar, D.K.1    Verkhivker, G.M.2    Rejto, P.A.3    Sherman, C.J.4    Fogel, D.B.5    Freer, S.T.6
  • 29
    • 0000882405 scopus 로고    scopus 로고
    • BLEEP - A potential of mean force describing protein-ligand interactions. II. Calculation of binding energies and comparison with experimental data
    • A new and interesting knowledge-based scoring function is described
    • Mitchell J.B.O., Laskowski R.A., Alex A., Forster M.J., Thornton J.M. BLEEP - a potential of mean force describing protein-ligand interactions. II. Calculation of binding energies and comparison with experimental data. J Comput Chem. 20:1999;1177-1185. A new and interesting knowledge-based scoring function is described.
    • (1999) J Comput Chem , vol.20 , pp. 1177-1185
    • Mitchell, J.B.O.1    Laskowski, R.A.2    Alex, A.3    Forster, M.J.4    Thornton, J.M.5
  • 30
    • 0033566211 scopus 로고    scopus 로고
    • Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein
    • Muegge I., Martin Y.C., Hajduk P.J., Fesik S.W. Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. J Med Chem. 42:1999;2498-2503.
    • (1999) J Med Chem , vol.42 , pp. 2498-2503
    • Muegge, I.1    Martin, Y.C.2    Hajduk, P.J.3    Fesik, S.W.4
  • 31
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • A promising new knowledge-based scoring function is described
    • Muegge I., Martin Y.C. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem. 42:1999;791-804. A promising new knowledge-based scoring function is described.
    • (1999) J Med Chem , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 32
    • 6244283606 scopus 로고    scopus 로고
    • Critical evaluation of search algorithms for automated molecular docking and database screening
    • Ewing T.J.A., Kuntz I.D. Critical evaluation of search algorithms for automated molecular docking and database screening. J Comput Chem. 18:1997;1175-1189.
    • (1997) J Comput Chem , vol.18 , pp. 1175-1189
    • Ewing, T.J.A.1    Kuntz, I.D.2
  • 33
    • 0033576680 scopus 로고    scopus 로고
    • Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
    • An important paper on the comparison of current scoring functions in virtual screening applications
    • Charifson P.S., Corkery J.J., Murcko M.A., Walters W.P. Consensus scoring: a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem. 42:1999;5100-5109. An important paper on the comparison of current scoring functions in virtual screening applications.
    • (1999) J Med Chem , vol.42 , pp. 5100-5109
    • Charifson, P.S.1    Corkery, J.J.2    Murcko, M.A.3    Walters, W.P.4
  • 34
    • 0032226476 scopus 로고    scopus 로고
    • Development of filter functions for protein-ligand docking
    • Stahl M., Böhm H.J. Development of filter functions for protein-ligand docking. J Mol Graph Model. 16:1998;121-132.
    • (1998) J Mol Graph Model , vol.16 , pp. 121-132
    • Stahl, M.1    Böhm, H.J.2
  • 35
    • 0032708785 scopus 로고    scopus 로고
    • Efficacy and selectivity in flexible database docking
    • Knegtel R.M.A., Wagener M. Efficacy and selectivity in flexible database docking. Proteins. 37:1999;334-345.
    • (1999) Proteins , vol.37 , pp. 334-345
    • Knegtel, R.M.A.1    Wagener, M.2
  • 36
    • 0032840569 scopus 로고    scopus 로고
    • DREAM++: Flexible docking program for virtual combinatorial libraries
    • Makino S., Ewing T.J.A., Kuntz I.D. DREAM++: flexible docking program for virtual combinatorial libraries. J Comput Aided Mol Des. 13:1999;513-532.
    • (1999) J Comput Aided Mol des , vol.13 , pp. 513-532
    • Makino, S.1    Ewing, T.J.A.2    Kuntz, I.D.3
  • 37
    • 0032836350 scopus 로고    scopus 로고
    • Structure-based drug design: Combinatorial chemistry and molecular modeling
    • Kirkpatrick D.L., Watson S., Ulhaq S. Structure-based drug design: combinatorial chemistry and molecular modeling. Comb Chem High Throughput Screen. 2:1999;211-221.
    • (1999) Comb Chem High Throughput Screen , vol.2 , pp. 211-221
    • Kirkpatrick, D.L.1    Watson, S.2    Ulhaq, S.3
  • 38
  • 39
    • 0033594354 scopus 로고    scopus 로고
    • Potent, low-molecular-weight non-peptide inhibitors of malarial aspartyl protease plasmepsin II
    • A recent paper from the Ellman and Kuntz group describing a successful application of combinatorial docking
    • Haque T.S., Skillman A.G., Lee C.E., Habashita H., Gluzman I.Y., Ewing T.J., Goldberg D.E., Kuntz I.D., Ellman J.A. Potent, low-molecular-weight non-peptide inhibitors of malarial aspartyl protease plasmepsin II. J Med Chem. 42:1999;1428-1440. A recent paper from the Ellman and Kuntz group describing a successful application of combinatorial docking.
    • (1999) J Med Chem , vol.42 , pp. 1428-1440
    • Haque, T.S.1    Skillman, A.G.2    Lee, C.E.3    Habashita, H.4    Gluzman, I.Y.5    Ewing, T.J.6    Goldberg, D.E.7    Kuntz, I.D.8    Ellman, J.A.9
  • 40
    • 0033530862 scopus 로고    scopus 로고
    • Blockers of human T cell Kv1.3 potassium channels using de novo ligand design and solid-phase parallel combinatorial chemistry
    • Lew A., Chamberlin A.R. Blockers of human T cell Kv1.3 potassium channels using de novo ligand design and solid-phase parallel combinatorial chemistry. Bioorg Med Chem Lett. 9:1999;3267-3272.
    • (1999) Bioorg Med Chem Lett , vol.9 , pp. 3267-3272
    • Lew, A.1    Chamberlin, A.R.2
  • 41
    • 0033585008 scopus 로고    scopus 로고
    • Using a galactose library for exploration of a novel hydrophobic pocket in the receptor binding site of the Escherichia coli heat-labile enterotoxin
    • Minke W.E., Hong F., Verlinde C.L., Hol W.G., Fan E. Using a galactose library for exploration of a novel hydrophobic pocket in the receptor binding site of the Escherichia coli heat-labile enterotoxin. J Biol Chem. 274:1999;33469-33473.
    • (1999) J Biol Chem , vol.274 , pp. 33469-33473
    • Minke, W.E.1    Hong, F.2    Verlinde, C.L.3    Hol, W.G.4    Fan, E.5
  • 42
    • 0026813925 scopus 로고
    • The computer program LUDI: A new method for the de novo design of enzyme inhibitors
    • Böhm H.J. The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J Comput Aided Mol Des. 6:1992;61-78.
    • (1992) J Comput Aided Mol des , vol.6 , pp. 61-78
    • Böhm, H.J.1
  • 43
    • 0033117680 scopus 로고    scopus 로고
    • Novel structural templates for estrogen-receptor ligands and prospects for combinatorial synthesis of estrogens
    • Fink B.E., Mortensen D.S., Stauffer S.R., Zachary D.A., Katzenellenbogen J.A. Novel structural templates for estrogen-receptor ligands and prospects for combinatorial synthesis of estrogens. Chem Biol. 6:1999;205-219.
    • (1999) Chem Biol , vol.6 , pp. 205-219
    • Fink, B.E.1    Mortensen, D.S.2    Stauffer, S.R.3    Zachary, D.A.4    Katzenellenbogen, J.A.5
  • 44
    • 0000864593 scopus 로고    scopus 로고
    • Recent developments in molecular diversity: Computational apporaches to combinatorial chemistry
    • Spellmeyer D.C., Grootenhuis P.D.J. Recent developments in molecular diversity: computational apporaches to combinatorial chemistry. Ann Rep Med Chem. 34:1999;287-296.
    • (1999) Ann Rep Med Chem , vol.34 , pp. 287-296
    • Spellmeyer, D.C.1    Grootenhuis, P.D.J.2
  • 45
    • 0033598416 scopus 로고    scopus 로고
    • Prospective identification of biologically active structures by topomer shape similarity searching
    • Cramer R.D., Poss M.A., Hermsmeier M.A., Caulfield T.J., Kowala M.C., Valentine M.T. Prospective identification of biologically active structures by topomer shape similarity searching. J Med Chem. 42:1999;3919-3933.
    • (1999) J Med Chem , vol.42 , pp. 3919-3933
    • Cramer, R.D.1    Poss, M.A.2    Hermsmeier, M.A.3    Caulfield, T.J.4    Kowala, M.C.5    Valentine, M.T.6
  • 46
    • 0033529045 scopus 로고    scopus 로고
    • SQ: A program for rapidly producing pharmacophorically relevant molecular superpositions
    • Miller M.D., Sheridan R.P., Kearsley S.K. SQ: a program for rapidly producing pharmacophorically relevant molecular superpositions. J Med Chem. 42:1999;1505-1514.
    • (1999) J Med Chem , vol.42 , pp. 1505-1514
    • Miller, M.D.1    Sheridan, R.P.2    Kearsley, S.K.3
  • 47
    • 0033606988 scopus 로고    scopus 로고
    • New 4-point pharmacophore method for molecular similarity and diversity applications: Overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures
    • Mason J.S., Morize I., Menard P.R., Cheney D.L., Hulme C., Labaudiniere R.F. New 4-point pharmacophore method for molecular similarity and diversity applications: overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures. J Med Chem. 42:1999;3251-3264.
    • (1999) J Med Chem , vol.42 , pp. 3251-3264
    • Mason, J.S.1    Morize, I.2    Menard, P.R.3    Cheney, D.L.4    Hulme, C.5    Labaudiniere, R.F.6
  • 48
    • 0033518275 scopus 로고    scopus 로고
    • Designing libraries with CNS activity
    • Ajay Bemis G.W., Murcko M.A. Designing libraries with CNS activity. J Med Chem. 42:1999;4942-4951.
    • (1999) J Med Chem , vol.42 , pp. 4942-4951
    • Ajay Bemis, G.W.1    Murcko, M.A.2
  • 49
    • 0033179183 scopus 로고    scopus 로고
    • Recognizing molecules with drug-like properties
    • Walters W.P., Ajay Murcko M.A. Recognizing molecules with drug-like properties. Curr Opin Chem Biol. 3:1999;384-387.
    • (1999) Curr Opin Chem Biol , vol.3 , pp. 384-387
    • Walters, W.P.1    Ajay Murcko, M.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.