Computational Drug Discovery and Design

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  1. Gillett VJ, Myatt G, Zsoldos Z, Johnson AP
    (1995) SPROUT, HIPPO and CAESA: tools
    for de novo structure generation and estima-
    tion of synthetic accessibility. Perspect Drug
    Discov Des 3:34–50

  2. Eisen MB, Wiley DC, Karplus M, Hubbard
    RE (1994) HOOK: a program for finding
    novel molecular architectures that satisfy the
    chemical and steric requirements of a macro-
    molecule binding site. Proteins 19:199–221

  3. Bohacek RS, McMartin C (1994) Multiple
    highly diverse structures complementary to
    enzyme binding sites: results of extensive
    application of ade novodesign method incor-
    porating combinatorial growth. J Am Chem
    Soc 116:5560–5571

  4. Glen RC, Payne AWR (1995) A genetic algo-
    rithm for the automated generation of mole-
    cules within constraints. J Comput Aided Mol
    Des 9:181–202

  5. Clark DE, Frenkel D, Levy SA, Li J, Murray
    CW, Robson B, Waszkowycz B, Westhead DR
    (1995) PRO-LIGAND: an approach tode
    novomolecular design. 1. Application to the
    design of organic molecules. J Comput Aided
    Mol Des 9:13–32

  6. Miranker A, Karplus M (1995) An automated
    method for dynamic ligand design. Proteins
    23:472–490

  7. DeWitte RS, Shakhnovich EI (1996) SMoG
    de novodesign method based on simple, fast,
    and accurate free energy estimates. 1. Method-
    ology and supporting evidence. J Am Chem
    Soc 118:11733–11744

  8. Pearlman DA, Murcko MA (1996) CON-
    CERTS: dynamic connection of fragments as
    an approach tode novoligand design. J Med
    Chem 39:1651–1663

  9. Luo Z, Wang R, Lai L (1996) RASSE: a new
    method for structure-based drug design. J
    Chem Inf Comput Sci 36:1187–1194

  10. Murray CW, Clark DE, Auton TR, Firth MA,
    Li J, Sykes RA, Waszkowycz B, Westhead DR,
    Young SC (1997) PRO_SELECT: combining
    structure-based drug design and combinato-
    rial chemistry for rapid lead discovery. 1. Tech-
    nology. J Comput Aided Mol Des
    11:193–207

  11. Todorov NP, Dean PM (1997) Evaluation of
    a method for controlling molecular scaffold
    diversity inde novoligand design. J Comput
    Aided Mol Des 11:175–192

  12. Nachbar RB (2000) Molecular evolution:
    automated manipulation of hierarchical
    chemical topology and its application to aver-
    age molecular structures. Genet Program
    Evolvable Mach 1:57–94
    57. Globus A, Lawton J, Wipke WT (1999) Auto-
    matic molecular design using evolutionary
    algorithms. Nanotechnology 10:290–299
    58. Liu H, Duan Z, Luo Q, Shi Y (1999) Struc-
    ture based ligand design by dynamically
    assembling molecular building blocks at bind-
    ing site. Proteins 36:462–470
    59. Douguet D, Thoreau E, Grassy G (2000) A
    genetic algorithm for the automated genera-
    tion of small organic molecules: drug design
    using an evolutionary algorithm. J Comput
    Aided Mol Des 14:449–466
    60. Wang R, Gao Y, Lai L (2000) LigBuilder: a
    multi-purpose program for structure-based
    drug design. J Mol Model 6:498–516
    61. Schneider G, Lee ML, Stahl M, Schneider P
    (2000)De novodesign of molecular architec-
    tures by evolutionary assembly of drug-
    derived building blocks. J Comput Aided
    Mol Des 14:487–494
    62. Zhu J, Fan H, Liu H, Shi Y (2001) Structure
    based ligand design for flexible proteins:
    application of new F-Dyco block. J Comput
    Aided Mol Des 15:979–996
    63. Pegg SCH, Haresco JJ, Kuntz ID (2001) A
    genetic algorithm for structure-basedde novo
    design. J Comput Aided Mol Des
    15:911–933
    64. Pellegrini E, Field MJ (2003) Development
    and testing of ade novodrug-design algo-
    rithm. J Comput Aided Mol Des 17:621–641
    65. Vinkers HM, de Jonge MR, Daeyaert FF,
    Heeres J, Koymans LM, van Lenthe JH,
    Lewi PJ, Timmerman H, Van Aken K, Janssen
    PA (2003) SYNOPSIS: SYNthesize and OPti-
    mize system in silico. J Med Chem
    46:2765–2773
    66. Brown N, McKay B, Gilardoni F, Gasteiger J
    (2004) A graph-based genetic algorithm and
    its application to the multi objective evolution
    of median molecules. J Chem Inf Comput Sci
    44:1079–1087
    67. Nikitin S, Zaitseva N, Demina O, Solovieva V,
    Mazin E, Mikhalev S, Smolov M, Rubinov A,
    Vlasov P, Lepikhin D, Khachko D, Fokin V,
    Queen C, Zosimov V (2005) A very large
    diversity space of synthetically accessible com-
    pounds for use with drug design programs. J
    Comput Aided Mol Des 19:47–63
    68. Douguet D, Munier-Lehmann H, Labesse G,
    Pochet S (2005) LEA3D: a computer-aided
    ligand design for structure-based drug design.
    J Med Chem 48:2457–2468
    69. Fechner U, Schneider G (2006) Flux (1): a
    virtual synthesis scheme for fragment basedde
    novodesign. J Chem Inf Model 46:699–707


84 Venkatesan Suryanarayanan et al.

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