메뉴 건너뛰기




Volumn 4, Issue 8, 2005, Pages 649-663

Computer-based de novo design of drug-like molecules

Author keywords

[No Author keywords available]

Indexed keywords

CANNABINOID 1 RECEPTOR; CYCLIN DEPENDENT KINASE 4; CYCLIN DEPENDENT KINASE INHIBITOR; LIGAND; PHOSPHOTRANSFERASE INHIBITOR; PROTEINASE INHIBITOR; RNA DIRECTED DNA POLYMERASE INHIBITOR; STEROL 14ALPHA DEMETHYLASE; THROMBIN INHIBITOR;

EID: 23844449940     PISSN: 14741776     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrd1799     Document Type: Review
Times cited : (784)

References (106)
  • 1
    • 11144341956 scopus 로고    scopus 로고
    • Chemical space and biology
    • Dobson, C. M. Chemical space and biology. Nature 432, 824-828 (2004).
    • (2004) Nature , vol.432 , pp. 824-828
    • Dobson, C.M.1
  • 2
    • 11144320699 scopus 로고    scopus 로고
    • Navigating chemical space for biology and medicine
    • Lipinski, C. & Hopkins, A. Navigating chemical space for biology and medicine. Nature 432, 855-861 (2004).
    • (2004) Nature , vol.432 , pp. 855-861
    • Lipinski, C.1    Hopkins, A.2
  • 3
    • 0036420691 scopus 로고    scopus 로고
    • Trends in virtual combinatorial library design
    • Schneider, G. Trends in virtual combinatorial library design. Curr. Med. Chem. 9, 2095-2101 (2002).
    • (2002) Curr. Med. Chem. , vol.9 , pp. 2095-2101
    • Schneider, G.1
  • 5
    • 1842347268 scopus 로고
    • Looking at proteins: Representations, folding, packing, and design
    • Richardson, J. S. et al. Looking at proteins: representations, folding, packing, and design. Biophys. J. 63, 1185-1209 (1992).
    • (1992) Biophys. J. , vol.63 , pp. 1185-1209
    • Richardson, J.S.1
  • 6
    • 0026345685 scopus 로고
    • Computer design of bioactive molecules: A method for receptor-based de novo ligand design
    • Moon, J. B. & Howe, W. J. Computer design of bioactive molecules: a method for receptor-based de novo ligand design. Proteins 11, 314-328 (1991).
    • (1991) Proteins , vol.11 , pp. 314-328
    • Moon, J.B.1    Howe, W.J.2
  • 7
    • 0027976928 scopus 로고
    • The rational design of amino acid sequences by artificial neural networks and simulated molecular evolution: De novo design of an idealized leader peptidase cleavage site
    • Schneider, G. & Wrede, P. The rational design of amino acid sequences by artificial neural networks and simulated molecular evolution: de novo design of an idealized leader peptidase cleavage site. Biophys. J. 66, 336-344 (1994).
    • (1994) Biophys. J. , vol.66 , pp. 336-344
    • Schneider, G.1    Wrede, P.2
  • 8
    • 0032514619 scopus 로고    scopus 로고
    • Peptide design by artificial neural networks and computer-based evolutionary search
    • Schneider, G. et al. Peptide design by artificial neural networks and computer-based evolutionary search. Proc. Natl Acad. Sci. USA 95, 12179-12184 (1998).
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 12179-12184
    • Schneider, G.1
  • 11
    • 0032202543 scopus 로고    scopus 로고
    • Parametric sensitivity and search-space characterization studies of genetic algorithms for computer-aided polymer design
    • Sundaram, A. & Venkatasubramanian, V. Parametric sensitivity and search-space characterization studies of genetic algorithms for computer-aided polymer design. J. Chem. Inf. Comput. Sci. 38, 1177-1191 (1998).
    • (1998) J. Chem. Inf. Comput. Sci. , vol.38 , pp. 1177-1191
    • Sundaram, A.1    Venkatasubramanian, V.2
  • 12
    • 0024549279 scopus 로고
    • Automated site-directed drug design: A general algorithm for knowledge acquisition about hydrogen-bonding regions at protein surfaces
    • Danziger, D. J. & Dean, P.M. Automated site-directed drug design: a general algorithm for knowledge acquisition about hydrogen-bonding regions at protein surfaces. Proc. R. Soc. Lond. B 236, 101-113 (1989).
    • (1989) Proc. R. Soc. Lond. B , vol.236 , pp. 101-113
    • Danziger, D.J.1    Dean, P.M.2
  • 13
    • 0026813925 scopus 로고
    • The computer program LUDI: A new simple method for the de-novo design of enzyme inhibitors
    • Böhm, H.-J. The computer program LUDI: a new simple method for the de-novo design of enzyme inhibitors. J. Comput. Aided Mol. Des. 6, 61-78 (1992).
    • (1992) J. Comput. Aided Mol. Des. , vol.6 , pp. 61-78
    • Böhm, H.-J.1
  • 14
    • 0027027467 scopus 로고
    • LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads
    • Böhm, H.-J. LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J. Comput. Aided Mol. Des. 6, 593-606 (1992).
    • (1992) J. Comput. Aided Mol. Des. , vol.6 , pp. 593-606
    • Böhm, H.-J.1
  • 15
    • 0029242576 scopus 로고
    • PRO LIGAND: An approach to de novo molecular design. 1. Application to the design of organic molecules
    • Clark, D. E. et al. PRO LIGAND: an approach to de novo molecular design. 1. Application to the design of organic molecules. J. Comput. Aided Mol. Des. 9, 13-32 (1995).
    • (1995) J. Comput. Aided Mol. Des. , vol.9 , pp. 13-32
    • Clark, D.E.1
  • 16
    • 0031087525 scopus 로고    scopus 로고
    • PRO_SELECT: Combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology
    • Murray, C. W. et al. PRO_SELECT: combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology. J. Comp. Aided Mol. Des. 11, 193-207 (1997).
    • (1997) J. Comp. Aided Mol. Des. , vol.11 , pp. 193-207
    • Murray, C.W.1
  • 17
    • 0002820943 scopus 로고
    • SPROUT, HIPPO and CAESA: Tools for de novo structure generation and estimation of synthetic accessibility
    • Gillett, V. J., Myatt, G., Zsoldos, Z. & Johnson, A. P. SPROUT, HIPPO and CAESA: tools for de novo structure generation and estimation of synthetic accessibility. Perspect. Drug Discov. Des. 3, 34-50 (1995).
    • (1995) Perspect. Drug Discov. Des. , vol.3 , pp. 34-50
    • Gillett, V.J.1    Myatt, G.2    Zsoldos, Z.3    Johnson, A.P.4
  • 18
    • 0027193713 scopus 로고
    • GroupBuild: A fragment-based method for de novo drug design
    • Rotstein, S. H. & Murcko, M. A. GroupBuild: a fragment-based method for de novo drug design. J. Med. Chem. 36, 1700-1710 (1993).
    • (1993) J. Med. Chem. , vol.36 , pp. 1700-1710
    • Rotstein, S.H.1    Murcko, M.A.2
  • 19
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 28, 849-857 (1985).
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 20
    • 0025988461 scopus 로고
    • Automatic creation of dug candidate structures based on receptor structure. Starting point for artificial lead generation
    • Nishibata, Y. & Itai, A. Automatic creation of dug candidate structures based on receptor structure. Starting point for artificial lead generation. Tetrahedron 47, 8985-8990 (1991).
    • (1991) Tetrahedron. , vol.47 , pp. 8985-8990
    • Nishibata, Y.1    Itai, A.2
  • 21
    • 0028036120 scopus 로고
    • Multiple highly diverse structures complementary to enzyme binding sites: Results of extensive application of a de novo design method incorporating combinatorial growth
    • Bohacek, R. S. & McMartin, C. Multiple highly diverse structures complementary to enzyme binding sites: results of extensive application of a de novo design method incorporating combinatorial growth. J. Am. Chem. Soc. 116, 5560-5571 (1994).
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 5560-5571
    • Bohacek, R.S.1    McMartin, C.2
  • 22
    • 0029285723 scopus 로고
    • A genetic algorithm for the automated generation of molecules within constraints
    • Glen, R. C. & Payne, A. W. R. A genetic algorithm for the automated generation of molecules within constraints. J. Comput. Aided. Mol. Des. 9, 181-202 (1995).
    • (1995) J. Comput. Aided. Mol. Des. , vol.9 , pp. 181-202
    • Glen, R.C.1    Payne, A.W.R.2
  • 23
    • 0030277958 scopus 로고    scopus 로고
    • RASSE: A new method for structure-based drug design
    • Luo, Z., Wang, R. & Lai, L. RASSE: a new method for structure-based drug design. J. Chem. Inf. Comput. Sci. 36, 1187-1194 (1996).
    • (1996) J. Chem. Inf. Comput. Sci. , vol.36 , pp. 1187-1194
    • Luo, Z.1    Wang, R.2    Lai, L.3
  • 24
    • 0000217414 scopus 로고    scopus 로고
    • LigBuilder: A multi-purpose program for structure-based drug design
    • Wang, R., Gao, Y. & Lai, L. LigBuilder: a multi-purpose program for structure-based drug design. J. Mol. Model. 6, 498-516 (2000).
    • (2000) J. Mol. Model. , vol.6 , pp. 498-516
    • Wang, R.1    Gao, Y.2    Lai, L.3
  • 25
    • 0028282687 scopus 로고
    • HOOK: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site
    • Eisen, M. B., Wiley, D.C., Karplus, M. & Hubbard, R. E. HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site. Proteins 19, 199-221 (1994).
    • (1994) Proteins , vol.19 , pp. 199-221
    • Eisen, M.B.1    Wiley, D.C.2    Karplus, M.3    Hubbard, R.E.4
  • 26
    • 0029586802 scopus 로고
    • An automated method for dynamic ligand design
    • Miranker, A. & Karplus, M. An automated method for dynamic ligand design. Proteins 23, 472-490 (1995).
    • (1995) Proteins , vol.23 , pp. 472-490
    • Miranker, A.1    Karplus, M.2
  • 27
    • 0025916872 scopus 로고
    • Functionality maps of binding sites: A multiple copy simultaneous search method
    • Miranker, A. & Karplus, M. Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins 11, 29-34 (1991).
    • (1991) Proteins , vol.11 , pp. 29-34
    • Miranker, A.1    Karplus, M.2
  • 28
    • 0026694615 scopus 로고
    • Automated site-directed drug design using molecular lattices
    • Lewis, R. A. et al. Automated site-directed drug design using molecular lattices. J. Mol. Graphics 10, 66-78 (1992).
    • (1992) J. Mol. Graphics , vol.10 , pp. 66-78
    • Lewis, R.A.1
  • 29
    • 0029320812 scopus 로고
    • BUILDER v.2: Improving the chemistry of a de novo design strategy
    • Roe, D. C. & Kuntz, I. D. BUILDER v.2: improving the chemistry of a de novo design strategy. J. Comput. Aided Mol. Des. 9, 269-282 (1995).
    • (1995) J. Comput. Aided Mol. Des. , vol.9 , pp. 269-282
    • Roe, D.C.1    Kuntz, I.D.2
  • 30
    • 0027136267 scopus 로고
    • The NEWLEAD program: A new method for the design of candidate structures from pharmacophoric hypothesis
    • Tschinke, V. & Cohen, N. C. The NEWLEAD program: a new method for the design of candidate structures from pharmacophoric hypothesis. J. Med. Chem. 36, 3863-3870 (1993).
    • (1993) J. Med. Chem. , vol.36 , pp. 3863-3870
    • Tschinke, V.1    Cohen, N.C.2
  • 31
    • 0024501968 scopus 로고
    • Automated site-directed drug design: The formation of molecular templates in primary structure generation
    • Lewis, R. A. & Dean, P. M. Automated site-directed drug design: the formation of molecular templates in primary structure generation. Proc. R. Soc. Lond. B 236, 141-162 (1989).
    • (1989) Proc. R. Soc. Lond. B , vol.236 , pp. 141-162
    • Lewis, R.A.1    Dean, P.M.2
  • 33
    • 0025440351 scopus 로고
    • Automated site-directed drug design: Approaches to the formation of 3D molecular graphs
    • Lewis, R. A. Automated site-directed drug design: approaches to the formation of 3D molecular graphs. J. Comput. Aided Mol. Des. 4, 205-210 (1990).
    • (1990) J. Comput. Aided Mol. Des. , vol.4 , pp. 205-210
    • Lewis, R.A.1
  • 35
    • 0029965861 scopus 로고    scopus 로고
    • CONCERTS: Dynamic connection of fragments as an approach to de novo ligand design
    • Pearlman, D. A. & Murcko, M. A. CONCERTS: dynamic connection of fragments as an approach to de novo ligand design. J. Med. Chem. 39, 1651-1663 (1996).
    • (1996) J. Med. Chem. , vol.39 , pp. 1651-1663
    • Pearlman, D.A.1    Murcko, M.A.2
  • 36
    • 0032769150 scopus 로고    scopus 로고
    • Structure-based ligand design by dynamically assembling molecular building blocks at binding site
    • Liu, H., Duan, Z., Luo, Q. & Shi, Y. Structure-based ligand design by dynamically assembling molecular building blocks at binding site. Proteins 36, 462-470 (1999).
    • (1999) Proteins , vol.36 , pp. 462-470
    • Liu, H.1    Duan, Z.2    Luo, Q.3    Shi, Y.4
  • 37
    • 0035003876 scopus 로고    scopus 로고
    • Design of selective inhibitors of cyclooxygenase-2 dynamic assembly of molecular building blocks
    • Zhu, J., Yu, H., Fan, H. Liu, H. & Shi, Y. Design of selective inhibitors of cyclooxygenase-2 dynamic assembly of molecular building blocks. J. Comput. Aided Mol. Des. 15, 447-463 (2001).
    • (2001) J. Comput. Aided Mol. Des. , vol.15 , pp. 447-463
    • Zhu, J.1    Yu, H.2    Fan, H.3    Liu, H.4    Shi, Y.5
  • 38
    • 0035731507 scopus 로고    scopus 로고
    • Structure-based ligand design for flexible proteins: Application of new F-DycoBlock
    • Zhu, J., Fan, H., Liu, H. & Shi, Y. Structure-based ligand design for flexible proteins: application of new F-DycoBlock. J. Comput. Aided Mol. Des. 15, 979-996 (2001).
    • (2001) J. Comput. Aided Mol. Des. , vol.15 , pp. 979-996
    • Zhu, J.1    Fan, H.2    Liu, H.3    Shi, Y.4
  • 39
    • 0348242299 scopus 로고
    • CONCEPTS: New dynamic algorithm for de novo design suggestion
    • Pearlman, D. A. & Murcko, M. A. CONCEPTS: new dynamic algorithm for de novo design suggestion. J. Comput. Chem. 14, 1184-1193 (1993).
    • (1993) J. Comput. Chem. , vol.14 , pp. 1184-1193
    • Pearlman, D.A.1    Murcko, M.A.2
  • 40
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • Eldridge, M.D., Murray, C. W., Auton, T. R., Paolini, G. V. & Mee, R. P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput. Aided Mol. Des. 11, 425-445 (1997).
    • (1997) J. Comput. Aided Mol. Des. , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 41
    • 0000934205 scopus 로고    scopus 로고
    • SMoG de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence
    • DeWitte, R. S. & Shakhnovich, E. I. SMoG de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence. J. Am. Chem. Soc. 118, 11733-11744 (1996).
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11733-11744
    • DeWitte, R.S.1    Shakhnovich, E.I.2
  • 42
    • 0037142298 scopus 로고    scopus 로고
    • SMall Molecule Growth 2001 (SMoG2001): An improved knowledge-based scoring function for protein-ligand interactions
    • Ishchenko, A. V. & Shakhnovich, E. I. SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions. J. Med. Chem. 45, 2770-2780 (2002).
    • (2002) J. Med. Chem. , vol.45 , pp. 2770-2780
    • Ishchenko, A.V.1    Shakhnovich, E.I.2
  • 43
    • 0037082324 scopus 로고    scopus 로고
    • Target validation of G-protein coupled receptors
    • Wise, A., Gearing, K. & Rees, S. Target validation of G-protein coupled receptors. Drug Discov. Today 7, 235-246 (2002).
    • (2002) Drug Discov. Today , vol.7 , pp. 235-246
    • Wise, A.1    Gearing, K.2    Rees, S.3
  • 44
    • 0028081385 scopus 로고
    • PRO LIGAND: An approach to de novo molecular design. 2. design of novel molecules from molecular field analysis (MFA) models and pharmacophores
    • Waszkowycz, B. et al. PRO LIGAND: an approach to de novo molecular design. 2. design of novel molecules from molecular field analysis (MFA) models and pharmacophores. J. Med. Chem. 37, 3994-4002 (1994).
    • (1994) J. Med. Chem. , vol.37 , pp. 3994-4002
    • Waszkowycz, B.1
  • 45
    • 0003913260 scopus 로고    scopus 로고
    • Molecular evolution: Automated manipulation of hierarchical chemical topology and its application to average molecular structures
    • Nachbar, R. B. Molecular evolution: automated manipulation of hierarchical chemical topology and its application to average molecular structures. Genet. Programming Evolvable Machines 1, 57-94 (2000).
    • (2000) Genet. Programming Evolvable Machines , vol.1 , pp. 57-94
    • Nachbar, R.B.1
  • 46
    • 1542608322 scopus 로고    scopus 로고
    • Development and testing of a de novo drug-design algorithm
    • Pellegrini, E. & Field, M. J. Development and testing of a de novo drug-design algorithm. J. Comp. Aided Mol. Des. 17, 621-641 (2003).
    • (2003) J. Comp. Aided Mol. Des. , vol.17 , pp. 621-641
    • Pellegrini, E.1    Field, M.J.2
  • 47
    • 0034085674 scopus 로고    scopus 로고
    • A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm
    • Douguet, D., Thoreau, E. & Grassy, G. A genetic algorithm for the automated generation of small organic molecules: drug design using an evolutionary algorithm. J. Comput. Aided Mol. Des. 14, 449-466 (2000).
    • (2000) J. Comput. Aided Mol. Des. , vol.14 , pp. 449-466
    • Douguet, D.1    Thoreau, E.2    Grassy, G.3
  • 48
    • 0034130399 scopus 로고    scopus 로고
    • De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks
    • Schneider, C., Lee, M.-L., Stahl, M. & Schneider, P. De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks. J. Comput. Aided Mol. Des. 14, 487-494 (2000).
    • (2000) J. Comput. Aided Mol. Des. , vol.14 , pp. 487-494
    • Schneider, C.1    Lee, M.-L.2    Stahl, M.3    Schneider, P.4
  • 49
    • 0032675130 scopus 로고    scopus 로고
    • Automatic Molecular design using evolutionary algorithms
    • Globus, A., Lawton, J. & Wipke, W. T. Automatic Molecular design using evolutionary algorithms. Nanotechnology 10, 290-299 (1999).
    • (1999) Nanotechnology , vol.10 , pp. 290-299
    • Globus, A.1    Lawton, J.2    Wipke, W.T.3
  • 50
    • 2942700379 scopus 로고    scopus 로고
    • A graph-based genetic algorithm and its application to the multiobjective evolution of median molecules
    • Brown, N., McKay, B., Gilardoni, F. & Gasteiger, J. A graph-based genetic algorithm and its application to the multiobjective evolution of median molecules. J. Chem. Inf. Comput. Sci. 44, 1079-1087 (2004).
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 1079-1087
    • Brown, N.1    McKay, B.2    Gilardoni, F.3    Gasteiger, J.4
  • 51
    • 0031024171 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • Lipinski, C. et al. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug. Deliv. Rev. 23, 3-25 (1997).
    • (1997) Adv. Drug Deliv. Rev. , vol.23 , pp. 3-25
    • Lipinski, C.1
  • 52
    • 0033576601 scopus 로고    scopus 로고
    • The design of leadlike combinatorial libraries
    • Teague, S. J. et al. The design of leadlike combinatorial libraries. Angew. Chem. Int. Ed. Engl. 38, 3743-3747 (1999).
    • (1999) Angew. Chem. Int. Ed. Engl. , vol.38 , pp. 3743-3747
    • Teague, S.J.1
  • 53
    • 13844254976 scopus 로고    scopus 로고
    • Predictive in silico modeling for hERG channel blockers
    • Aronov, A. M. Predictive in silico modeling for hERG channel blockers. Drug Discov. Today 10, 149-155 (2005).
    • (2005) Drug Discov. Today , vol.10 , pp. 149-155
    • Aronov, A.M.1
  • 54
    • 0032058905 scopus 로고    scopus 로고
    • RECAP - Retrosynthetic Combinatorial Analysis Procedure: A powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry
    • Lewell, X. O., Budd, D. B., Watson, S. P. & Hann, M. M. RECAP - Retrosynthetic Combinatorial Analysis Procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry. J. Chem. Inf. Comput. Sci. 38, 511-522 (1998).
    • (1998) J. Chem. Inf. Comput. Sci. , vol.38 , pp. 511-522
    • Lewell, X.O.1    Budd, D.B.2    Watson, S.P.3    Hann, M.M.4
  • 55
    • 0037777697 scopus 로고    scopus 로고
    • SYNOPSIS: SYNthesize and OPtimize System in Silico
    • Vinkers, H. M. et al. SYNOPSIS: SYNthesize and OPtimize System in Silico. J. Med. Chem. 46, 2765-2773 (2003).
    • (2003) J. Med. Chem. , vol.46 , pp. 2765-2773
    • Vinkers, H.M.1
  • 56
    • 0035924235 scopus 로고    scopus 로고
    • Structure-based generation of a new class of potent Cdk4 inhibitors: New de novo design strategy and library design
    • Honma, T. et al. Structure-based generation of a new class of potent Cdk4 inhibitors: new de novo design strategy and library design. J. Med. Chem. 44, 4615-4627 (2001).
    • (2001) J. Med. Chem. , vol.44 , pp. 4615-4627
    • Honma, T.1
  • 58
    • 0028167547 scopus 로고
    • P. SPROUT: Recent developments in the de novo design of molecules
    • Gillet, V. et al. P. SPROUT: recent developments in the de novo design of molecules. J. Chem. Inf. Comput. Sci. 34, 207-217 (1994).
    • (1994) J. Chem. Inf. Comput. Sci. , vol.34 , pp. 207-217
    • Gillet, V.1
  • 59
    • 0001125111 scopus 로고
    • SPROUT: 3D structure generation using templates
    • Mata, P. et al. SPROUT: 3D structure generation using templates. J. Chem. Inf. Comput. Sci. 35, 479-493 (1995).
    • (1995) J. Chem. Inf. Comput. Sci. , vol.35 , pp. 479-493
    • Mata, P.1
  • 60
    • 0001391169 scopus 로고
    • SPLICE: A program to assemble partial query solutions from three-dimensional database searches into novel ligands
    • Ho, C. M. W. & Marshall, C. R. SPLICE: a program to assemble partial query solutions from three-dimensional database searches into novel ligands. J. Comput. Aided Mol. Des. 7, 623-647 (1993).
    • (1993) J. Comput. Aided Mol. Des. , vol.7 , pp. 623-647
    • Ho, C.M.W.1    Marshall, C.R.2
  • 61
    • 0029062889 scopus 로고
    • De novo design of enzyme inhibitors by monte carlo ligand generation
    • Gelhaar, D. K. et al. De novo design of enzyme inhibitors by monte carlo ligand generation. J. Med. Chem. 38, 466-472 (1995).
    • (1995) J. Med. Chem. , vol.38 , pp. 466-472
    • Gelhaar, D.K.1
  • 62
    • 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. 47, 2768-2775 (2004).
    • (2004) J. Med. Chem. , vol.47 , pp. 2768-2775
    • Pierce, A.C.1    Rao, G.2    Bemis, G.W.3
  • 63
    • 0031088353 scopus 로고    scopus 로고
    • Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design
    • Todorov, N. P. & Dean, P. M. Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design. J. Comput. Aided. Mol. Des. 11, 175-192 (1997).
    • (1997) J. Comput. Aided. Mol. Des. , vol.11 , pp. 175-192
    • Todorov, N.P.1    Dean, P.M.2
  • 64
    • 0032111471 scopus 로고    scopus 로고
    • A branch-end-bound method for optimal atom-type assignment in de novo ligand design
    • Todorov, N. P. & Dean, P. M. A branch-end-bound method for optimal atom-type assignment in de novo ligand design. J. Comput. Aided. Mol. Des. 12, 335-350 (1998).
    • (1998) J. Comput. Aided. Mol. Des. , vol.12 , pp. 335-350
    • Todorov, N.P.1    Dean, P.M.2
  • 65
    • 0004034745 scopus 로고
    • (Facsimile of the First Edition) (Harvard Univ. Press, Cambridge, Massachusetts)
    • Darwin, C. On the Origin of Species (Facsimile of the First Edition) (Harvard Univ. Press, Cambridge, Massachusetts, 1859/1975).
    • (1859) On the Origin of Species
    • Darwin, C.1
  • 66
    • 0023965741 scopus 로고
    • SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
    • Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28, 31-36 (1988).
    • (1988) J. Chem. Inf. Comput. Sci. , vol.28 , pp. 31-36
    • Weininger, D.1
  • 68
    • 0036007208 scopus 로고    scopus 로고
    • Virtual screening and fast automated docking methods
    • Schneider, G. & Böhm, H.-J. Virtual screening and fast automated docking methods. Drug Discov. Today 7, 64-70 (2002).
    • (2002) Drug Discov. Today , vol.7 , pp. 64-70
    • Schneider, G.1    Böhm, H.-J.2
  • 69
    • 1642350394 scopus 로고    scopus 로고
    • Recent development and application of virtual screening in drug discovery: An overview
    • Hou, T. & Xu, X. Recent development and application of virtual screening in drug discovery: an overview. Curr. Pharm. Des. 10, 1011-1033 (2004).
    • (2004) Curr. Pharm. Des. , vol.10 , pp. 1011-1033
    • Hou, T.1    Xu, X.2
  • 70
    • 0041418274 scopus 로고    scopus 로고
    • Recent advances in de novo design strategy for practical lead identification
    • Honma, T. Recent advances in de novo design strategy for practical lead identification. Med. Res. Rev. 23, 606-632 (2003).
    • (2003) Med. Res. Rev. , vol.23 , pp. 606-632
    • Honma, T.1
  • 71
    • 0037434588 scopus 로고    scopus 로고
    • Structure-based de novo design, synthesis, and biological evaluation of non-azole inhibitors specific for lanosterol 14α-demethylase of fungi
    • Ji, H. et al. Structure-based de novo design, synthesis, and biological evaluation of non-azole inhibitors specific for lanosterol 14α-demethylase of fungi. J. Med. Chem. 46, 474-485 (2003).
    • (2003) J. Med. Chem. , vol.46 , pp. 474-485
    • Ji, H.1
  • 72
    • 3042806401 scopus 로고    scopus 로고
    • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
    • Perola, E., Walters, W. P. & Charifson, P. S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 56, 235-249 (2003).
    • (2003) Proteins , vol.56 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 73
    • 9344242435 scopus 로고    scopus 로고
    • Molecular diversity management strategies for building and enhancement of diverse and focused lead discovery compound screening collections
    • Schuffenhauer, A. et al. Molecular diversity management strategies for building and enhancement of diverse and focused lead discovery compound screening collections. Comb. Chem. High Throughput Screen. 7, 771-781 (2004).
    • (2004) Comb. Chem. High Throughput Screen , vol.7 , pp. 771-781
    • Schuffenhauer, A.1
  • 74
    • 0035924240 scopus 로고    scopus 로고
    • A novel approach for the development of selective Cdk4 inhibitors: Library design based on locations of Cdk4 specific amino acid residues
    • Honma, T. et al. A novel approach for the development of selective Cdk4 inhibitors: library design based on locations of Cdk4 specific amino acid residues. J. Med. Chem. 44, 4628-4640 (2001).
    • (2001) J. Med. Chem. , vol.44 , pp. 4628-4640
    • Honma, T.1
  • 75
    • 8544222806 scopus 로고    scopus 로고
    • Identification of novel cannabinoid receptor ligands via evolutionary de novo design and rapid parallel synthesis
    • Rogers-Evans, M., Alanine, A. I., Bleicher, K. H., Kube, D. & Schneider, G. Identification of novel cannabinoid receptor ligands via evolutionary de novo design and rapid parallel synthesis. QSAR Comb. Sci. 23, 426-430 (2004).
    • (2004) QSAR Comb. Sci. , vol.23 , pp. 426-430
    • Rogers-Evans, M.1    Alanine, A.I.2    Bleicher, K.H.3    Kube, D.4    Schneider, G.5
  • 76
    • 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, 51-56 (1999).
    • (1999) J. Comput. Aided Mol. Des. , vol.13 , pp. 51-56
    • Böhm, H.-J.1    Banner, D.W.2    Weber, L.3
  • 77
    • 0031128227 scopus 로고    scopus 로고
    • Molecular recognition at the thrombin active site: Structure-based design and synthesis of potent and selective thrombin inhibitors and tha X-ray crystal structures of two thrombin-inhibitor complexes
    • Obst, U., Banner, D. W., Weber, L. & Diederich, F. Molecular recognition at the thrombin active site: structure-based design and synthesis of potent and selective thrombin inhibitors and tha X-ray crystal structures of two thrombin-inhibitor complexes. Chem. Biol. 4, 287-295 (1997).
    • (1997) Chem. Biol. , vol.4 , pp. 287-295
    • Obst, U.1    Banner, D.W.2    Weber, L.3    Diederich, F.4
  • 78
    • 0037663879 scopus 로고    scopus 로고
    • A fluorine scan of thrombin inhibitors to map the fluorophilicity/fluorophobicity of an enzyme active site: Evidence for C-F...C=O interactions
    • Olsen, J. A. et al. A fluorine scan of thrombin inhibitors to map the fluorophilicity/fluorophobicity of an enzyme active site: evidence for C-F...C=O interactions. Angew. Chem. Int. Ed. Eng. 42, 2507-2511 (2003).
    • (2003) Angew Chem. Int. Ed. Eng. , vol.42 , pp. 2507-2511
    • Olsen, J.A.1
  • 79
    • 12844283957 scopus 로고    scopus 로고
    • High-throughput drug discovery: What can we expect from HTS?
    • Gribbon, P. & Sewing A., High-throughput drug discovery: what can we expect from HTS? Drug Discov. Today 10, 17-22 (2005).
    • (2005) Drug Discov. Today , vol.10 , pp. 17-22
    • Gribbon, P.1    Sewing, A.2
  • 80
    • 33645204379 scopus 로고    scopus 로고
    • The design and docking of virtual compound libraries to structures of drug targets
    • Anderson, A. C. & Wright, D. L. The design and docking of virtual compound libraries to structures of drug targets. Curr. Comp. Aided Drug Des. 1, 103-127 (2005).
    • (2005) Curr. Comp. Aided Drug Des. , vol.1 , pp. 103-127
    • Anderson, A.C.1    Wright, D.L.2
  • 82
    • 0029894013 scopus 로고    scopus 로고
    • The properties of known drugs. 1. Molecular frameworks
    • Bemis, G. W. & Murcko, M. A. The properties of known drugs. 1. Molecular frameworks. J. Med. Chem. 39, 2887-2893 (1996).
    • (1996) J. Med. Chem. , vol.39 , pp. 2887-2893
    • Bemis, G.W.1    Murcko, M.A.2
  • 83
    • 22844444644 scopus 로고    scopus 로고
    • (eds Kubinyi, H. & Müller, G.) (Wiley-VCH, Weinheim)
    • Müller, G. in Chemogenomics in Drug Discovery (eds Kubinyi, H. & Müller, G.) 7-41 (Wiley-VCH, Weinheim, 2004).
    • (2004) Chemogenomics in Drug Discovery , pp. 7-41
    • Müller, G.1
  • 84
    • 9744222830 scopus 로고    scopus 로고
    • A 3D similarity method for scaffold hopping from known drugs or natural ligands to new chemotypes
    • Jenkins, J. L., Glick, M. & Davies, J. W. A 3D similarity method for scaffold hopping from known drugs or natural ligands to new chemotypes. J. Med. Chem. 47, 6144-6159 (2004).
    • (2004) J. Med. Chem. , vol.47 , pp. 6144-6159
    • Jenkins, J.L.1    Glick, M.2    Davies, J.W.3
  • 85
    • 0035145264 scopus 로고    scopus 로고
    • High-throughput chemistry and structure-based design: Survival of the smartest
    • Bailey, D. & Brown, D. High-throughput chemistry and structure-based design: survival of the smartest. Drug Discov. Today 6, 57-59 (2001).
    • (2001) Drug Discov. Today , vol.6 , pp. 57-59
    • Bailey, D.1    Brown, D.2
  • 86
  • 87
    • 3342966009 scopus 로고    scopus 로고
    • Using NMR for ligand discovery and optimization
    • Villar, H. O., Yan, J. & Hansen, M. R. Using NMR for ligand discovery and optimization. Curr. Opin. Chem. Biol. 8, 387-391 (2004).
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 387-391
    • Villar, H.O.1    Yan, J.2    Hansen, M.R.3
  • 90
    • 0032015039 scopus 로고    scopus 로고
    • Superposition of three-dimensional chemical structures allowing for conformational flexibility by a hybrid method
    • Handschuh, S., Wagener, M. & Gasteiger, J. Superposition of three-dimensional chemical structures allowing for conformational flexibility by a hybrid method. J. Chem. Inf. Comput. Sci. 38, 220-232 (1998).
    • (1998) J. Chem. Inf. Comput. Sci. , vol.38 , pp. 220-232
    • Handschuh, S.1    Wagener, M.2    Gasteiger, J.3
  • 91
    • 0035327169 scopus 로고    scopus 로고
    • Multiobjective optimisation of combinatorial libraries
    • Agrafiotis, D. K. Multiobjective optimisation of combinatorial libraries. IBM J. Res. DeV. 45, 545-566 (2001).
    • (2001) IBM J. Res. DeV. , vol.45 , pp. 545-566
    • Agrafiotis, D.K.1
  • 93
    • 0029083247 scopus 로고
    • Design, synthesis and X-ray crystallographic studies of novel FKBB-12 ligands
    • Babine, R. E. et al. Design, synthesis and X-ray crystallographic studies of novel FKBB-12 ligands. Bioorg. Med. Chem. Lett. 5, 1719-1724 (1995).
    • (1995) Bioorg. Med. Chem. Lett. , vol.5 , pp. 1719-1724
    • Babine, R.E.1
  • 94
    • 0034665713 scopus 로고    scopus 로고
    • Structural mechanism of STI-571 inhibition of Abelson tyrosine kinase
    • Schindler, T. et al. Structural mechanism of STI-571 inhibition of Abelson tyrosine kinase. Science 289, 1938-1942 (2000).
    • (2000) Science , vol.289 , pp. 1938-1942
    • Schindler, T.1
  • 95
    • 0024503067 scopus 로고
    • Automated site-directed drug design: The concept of spacer skeletons for primary structure generation
    • Lewis, R. A. & Dean, P. M. Automated site-directed drug design: the concept of spacer skeletons for primary structure generation. Proc. R. Soc. Lond. B 236, 125-140 (1989).
    • (1989) Proc. R. Soc. Lond. B , vol.236 , pp. 125-140
    • Lewis, R.A.1    Dean, P.M.2
  • 96
    • 0027658106 scopus 로고
    • A novel computational tool for automated structure-based drug design
    • Böhm, H.-J. A novel computational tool for automated structure-based drug design. J. Mol. Recognit. 6, 131-137 (1993).
    • (1993) J. Mol. Recognit. , vol.6 , pp. 131-137
    • Böhm, H.-J.1
  • 97
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • Böhm, H.-J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput. Aided Mol. Des. 8, 243-256 (1994).
    • (1994) J. Comput. Aided Mol. Des. , vol.8 , pp. 243-256
    • Böhm, H.-J.1
  • 98
    • 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, 309-323 (1998).
    • (1998) J. Comput. Aided Mol. Des. , vol.12 , pp. 309-323
    • Böhm, H.-J.1
  • 99
    • 0034257202 scopus 로고    scopus 로고
    • Dynamic ligand design and combinatorial optimization: Designing inhibitors to endothiapepsin
    • Stultz, C. M. & Karplus, M. Dynamic ligand design and combinatorial optimization: designing inhibitors to endothiapepsin. Proteins 40, 258-289 (2000).
    • (2000) Proteins , vol.40 , pp. 258-289
    • Stultz, C.M.1    Karplus, M.2
  • 100
    • 0029281478 scopus 로고
    • PRO LIGAND: An approach to de novo molecular design. 3. A genetic algorithm for structure refinement
    • Westhead, D. R. et al. PRO LIGAND: an approach to de novo molecular design. 3. A genetic algorithm for structure refinement. J. Comput. Aided Mol. Des. 9, 139-148 (1995).
    • (1995) J. Comput. Aided Mol. Des. , vol.9 , pp. 139-148
    • Westhead, D.R.1
  • 101
    • 0029320501 scopus 로고
    • PRO LIGAND: An approach de novo molecular design. 4. Application to the design of peptides
    • Frenkel, D. et al. PRO LIGAND: an approach de novo molecular design. 4. Application to the design of peptides. J. Comput. Aided Mol. Des. 9, 213-225 (1995).
    • (1995) J. Comput. Aided Mol. Des. , vol.9 , pp. 213-225
    • Frenkel, D.1
  • 102
    • 0345522652 scopus 로고
    • PRO LIGAND: An approach to de novo molecular design. 5. Tools for the Analysis of Generated Structures
    • Clark, D. E. & Murray, C. W. PRO LIGAND: an approach to de novo molecular design. 5. Tools for the Analysis of Generated Structures. J. Chem. Inf. Comput. Sci. 35, 914-923 (1995).
    • (1995) J. Chem. Inf. Comput. Sci. , vol.35 , pp. 914-923
    • Clark, D.E.1    Murray, C.W.2
  • 103
    • 0029385233 scopus 로고
    • PRO LIGAND: An approach to de novo molecular design. 6. Flexible fitting in the design of peptides
    • Murray C. W., Clark, D. E., Byrne, D. G. PRO LIGAND: an approach to de novo molecular design. 6. Flexible fitting in the design of peptides. J. Comput. Aided Mol. Des. 9, 381-395 (1995).
    • (1995) J. Comput. Aided Mol. Des. , vol.9 , pp. 381-395
    • Murray, C.W.1    Clark, D.E.2    Byrne, D.G.3
  • 104
    • 0037022302 scopus 로고    scopus 로고
    • Combinatorial computational method gives new picomolar ligands for a known enzyme
    • Grzybowski, B. A. et al. Combinatorial computational method gives new picomolar ligands for a known enzyme. Proc. Natl Acad. Sci. USA 99, 1270-1273 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1270-1273
    • Grzybowski, B.A.1
  • 105
    • 0011137935 scopus 로고    scopus 로고
    • Molecular evolution: A hierarchical representation for chemical topology and its automated manipulation
    • (Univ. of Wisconsin, Madison, Wisconsin)
    • Nachbar, R. B. Molecular evolution: a hierarchical representation for chemical topology and its automated manipulation. Proc. 3rd Ann. Genetic Programming Conf. 246-253 (Univ. of Wisconsin, Madison, Wisconsin 1998).
    • (1998) Proc. 3rd Ann. Genetic Programming Conf. , pp. 246-253
    • Nachbar, R.B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.