Automated docking of highly flexible ligands by genetic algorithms: A critical assessment

被引：49
作者：
Cecchini, M [1 ]
Kolb, P [1 ]
Majeux, N [1 ]
Caflisch, A [1 ]
机构：
[1] Univ Zurich, Dept Biochem, CH-8057 Zurich, Switzerland
来源：
JOURNAL OF COMPUTATIONAL CHEMISTRY | 2004年 / 25卷 / 03期
关键词：
docking; genetic algorithm; SEED; FFLD; ligand flexibility; HIV-1; protease;
D O I：
10.1002/jcc.10384
中图分类号：
O6 [化学];
学科分类号：
0703 ;
摘要：
An improved version of the fragment-based flexible ligand docking approach SEED-FFLD is tested on inhibitors of human immunodeficiency virus type 1 protease, human alpha-thrombin and the estrogen receptor beta. The docking results indicate that it is possible to correctly reproduce the binding mode of inhibitors with more than ten rotatable bonds if the strain in their covalent geometry upon binding is not large. A high degree of convergence towards a unique binding mode in multiple runs of the genetic algorithm is proposed as a necessary condition for successful docking. (C) 2003 Wiley Periodicals, Inc.
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收藏
页码：412 / 422
页数：11
相关论文
共 54 条
  • [1] Apostolakis J, 1999, COMB CHEM HIGH T SCR, V2, P91
  • [2] Apostolakis J, 1998, J COMPUT CHEM, V19, P21, DOI 10.1002/(SICI)1096-987X(19980115)19:1<21::AID-JCC2>3.0.CO
  • [3] 2-0
  • [4] STRUCTURAL BASIS OF DRUG-RESISTANCE FOR THE V82A MUTANT OF HIV-1 PROTEINASE
    BALDWIN, ET
    BHAT, TN
    LIU, BS
    PATTABIRAMAN, N
    ERICKSON, JW
    [J]. NATURE STRUCTURAL BIOLOGY, 1995, 2 (03): : 244 - 249
  • [5] The Protein Data Bank
    Berman, HM
    Westbrook, J
    Feng, Z
    Gilliland, G
    Bhat, TN
    Weissig, H
    Shindyalov, IN
    Bourne, PE
    [J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 235 - 242
  • [6] CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS
    BROOKS, BR
    BRUCCOLERI, RE
    OLAFSON, BD
    STATES, DJ
    SWAMINATHAN, S
    KARPLUS, M
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) : 187 - 217
  • [7] Structure-based ligand design by a build-up approach and genetic algorithm search in conformational space
    Budin, N
    Majeux, N
    Tenette-Souaille, C
    Caflisch, A
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2001, 22 (16) : 1956 - 1970
  • [8] Fragment-based flexible ligand docking by evolutionary optimization
    Budin, N
    Majeux, N
    Caflisch, A
    [J]. BIOLOGICAL CHEMISTRY, 2001, 382 (09) : 1365 - 1372
  • [9] Synthesis and application of functionally diverse 2,6,9-trisubstituted purine libraries as CDK inhibitors
    Chang, YT
    Gray, NS
    Rosania, GR
    Sutherlin, DP
    Kwon, S
    Norman, TC
    Sarohia, R
    Leost, M
    Meijer, L
    Schultz, PG
    [J]. CHEMISTRY & BIOLOGY, 1999, 6 (06): : 361 - 375
  • [10] FlexE: Efficient molecular docking considering protein structure variations
    Claussen, H
    Buning, C
    Rarey, M
    Lengauer, T
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 2001, 308 (02) : 377 - 395
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