中文
Announcement
More
Progress in Chemistry 2004, Vol. 16 Issue (01): 35- Previous Articles   Next Articles

Special Issue: 计算化学

• Review •

Applications of Genetic Algorithms to Computer-Aided Drug Design

Hou Tingjun;Xu Xiaojie*   

  1. (College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China)
  • Received: Revised: Online: Published:
  • Contact: Xu Xiaojie
PDF ( 2729 ) Cited
Export

EndNote

Ris

BibTeX

As an important heuristic optimization algorithm, genetic algorithm (GA) has been widely applied in computer-aided drug design (CADD). In this paper, the basic concept and mechanism of GA were introduced. More-over, combining the research work in authors' group, the applications of GA in quantitative structure-activity relation-ship, conformational analysis, pharmacophore modeling, molecular docking and virtual combinatorial chemistry, were re-viewed.

CLC Number: 

[ 1 ] De Jong K A. Dissertation Abstracts International , 36 ( 10 ) :5140B. (University Microfilms no. 76 —9381)
[ 2 ] Holland J H. Adaptation in Natural and Artificial Systems. Ann Arbor : University of Michigan Press , 1975
[ 3 ] Leardi R , Boggia R , Terrile M. J . Chemom. , 1992 , 6 : 267 —281
[ 4 ] Leardi R. J . Chemom. , 1994 , 8 : 65 —79
[ 5 ] Rogers D , Hopfinger A J . J . Chem. Inf . Comp. Sci . , 1994 ,34 : 854 —866
[ 6 ] Luke B T. J . Chem. Inf . Comp. Sci . , 1994 , 34 : 1279 —1287
[ 7 ] Kubinyi H. Quant . Struct .-Act . Rel . , 1994 , 13 : 285 —294
[ 8 ] Kubinyi H. Quant . Struct .-Act . Rel . , 1994 , 13 : 393 —401
[ 9 ] So S S , Karplus M. J . Med. Chem. , 1996 , 39 : 1521 —1530
[10] So S S , Karplus M. J . Med. Chem. , 1996 , 39 : 5246 —5256
[11] Hou T J , Liao N , Luo H P , Xu X J . Chinese Chem. Lett . ,1999 , 10 : 759 —762
[12] Hou T J , Wang J M, Xu X J . Chemometr. Intell . Lab. , 1999 ,45 : 303 —310
[13] Hou T J , Wang J M, Liao N , Xu X J . J . Chem. Inf . Comp.Sci . , 1999 , 39 : 775 —781
[14] Hopfinger A J , Wang S , Tokarski J S. J . Am. Chem. Soc. ,1997 , 119 : 10509 —10524
[15] Albuquerque M G, Hopfinger A J , Barreiro EJ , de Alencastro R B. J . Chem. Inf . Comput . Sci . , 1998 , 38 : 925 —938
[16] Hou T J , Liao N , Luo H P , Xu X J . Chinese Chem. Lett . ,1999 , 10 : 759 —762
[17] Hou T J , Xu X J . J . Mol . Graph. Model . , 2001 , 19 : 455 —465
[18] Kimura T, Hasegawa K, Funatsu K. J . Chem. Inf . Comput .Sci . , 1998 , 38 : 276 —282
[19] Hasegawa K, Kimura T, Funatsu F. J . Chem. Inf . Comput .Sci . , 1999 , 39 : 112 —120
[20] Walters D E , Muhammad T D. Genetic Algorithms in Molecular Modelling(ed. Devillers J ) . Academic Press , 1996. 193 —210
[21] Walters D E , Hinds R M. J . Med. Chem. , 1994 , 37 : 2527 —2536
[22] Jones G, Willett P , Glen R C. J . Comput . Aid. Mol . Des. ,1995 , 9 : 532 —549
[23] Holliday J D , Willett P. Journal of Molecular Graphics and Model ling , 1997 , 15 : 221 —232
[24] Xiao Y L , Williams D E. J . Phys. Chem. , 1994 , 98 : 7191 —7200
[25] Oshiro C M, Kuntz I D , Dixon J S. J . Comput . Aid. Mol .Des. , 1995 , 9 : 113 —120
[26] Judson R S , Tan Y T, Mori E , Melius C , Jaeger E P , Treasurywala A M, Mathiowetz A. J . Comput . Chem. , 1995 , 16 :1405 —1419
[27] Jones G, Willett P , Glen R C. J . Mol . Biol . , 1995 , 245 : 43 —53
[28] Clark K P. J . Comput . Chem. , 1995 , 16 : 1210 —1226
[29] Verkhivker G M, Rejto P A , Gehlhaar D K, Freer S T. Proteins :Structure , Function and Genetics , 1996 , 25 : 342 —353
[30] Jones G, Willett P , Glen R C , Leach A R , Taylor R. J . Mol .Biol . , 1997 , 267 : 727 —748
[31] Ewing T J A , Kuntz I D. J . Comput . Chem. , 1997 , 18 : 1175 —1189
[32] Apostolakis J , Pluckthun A , Caflisch A. J . Comput . Chem. ,1998 , 19 : 21 —37
[33] Morris G M, Goodsell D S , Halliday R S , Huey R , Hart W E ,Belew R K, Olson A J . J . Comput . Chem. , 1998 , 19 : 1639 —1662
[34] Wang J M, Hou T J , Chen L R , Xu X J . Chemometr. Intell .Lab. , 1999 , 45 : 281 —286
[35] Hou T J , Wang J M, Xu X J . Chinese Chem. Lett . , 1999 , 10 :615 —618
[36] Hou T J , Wang J M, Chen L R , Xu X J . Protein Eng. , 1999 ,12 : 639 —647
[37] Yang J M, Kao C Y. J . Comput . Chem. , 2000 , 21 : 988 —998
[38] Taylor J S , Burnett R M. Proteins , 2000 , 41 : 173 —191
[39] Gardiner E J , Willett P , Artymiuk P J . Proteins , 2001 , 44 : 44 —56
[40] Thormann M, Pons M. J . Comput . Chem. , 2001 , 22 : 1971 —1982
[41] Judson R S , Jaeger E P , Treasurywala A M, Peterson M L. J .Comput . Chem. , 1993 , 14 : 1407 —1414
[42] McGarrah D B , Judson R S. J . Comput . Chem. , 1993 , 14 :1385 —1395
[43] Brodmeier T, Pretsch E. J . Comput . Chem. , 1994 , 15 : 588 —595
[44] Clark D E , Jones G, Willett P , Kenny P W, Glen R C. Journal of Chemical Information and Computer Sciences , 1994 , 34 : 197 —206
[45] Herrmann F , Suhai S. J . Comput . Chem. , 1995 , 16 : 1434 —1444
[46] Meza J C , Judson R S , Faulkner T R , Treasurywala A M. J .Comput . Chem. , 1996 , 17 : 1142 —1151
[47] Head M S , Given J A , Gilson M K. J . Phys. Chem. A , 1997 ,101 : 1609 —1618
[48] Jin A Y, Leung F Y, Weaver D F. J . Comput . Chem. , 1997 ,18 : 1971 —1984
[49] Wehrens R , Pretsch E , Buydens L M C. Journal of Chemical Information and Computer Sciences , 1998 , 38 : 151 —157
[50] Nair N , Goodman J M. J . Chem. Inf . Comp. Sci . , 1998 , 38 :317 —320
[51] Wang J M, Hou T J , Chen L R , Xu X J . Chemometr. Intell .Lab. , 1999 , 45 : 347 —351
[52] Mekenyan O , Dimitrov D , Nikolova N , Karabunarliev S. Journal of Chemical Information and Computer Sciences , 1999 , 39 : 997 —1016
[53] Jin A Y, Leung F Y, Weaver D F. J . Comput . Chem. , 1999 ,13 : 1329 —1342
[54] Bungay S D , Poirier R A , Charron R J . J . Math. Chem. , 2000 ,28 : 389 —401
[55] Sheridan R P , Kearsley S K. J . Chem. Inf . Comp. Sci . , 1995 ,35 : 310 —320
[56] Holland J D , Ranade S S , Willett P. Quantitative Structure-Activity Relationships , 1995 , 14 : 501 —506
[57] Yokobayashi Y, Ikebukuro I , McNiven S , Karube I. Journal of the Chemical Society-Perkin Transactions 1 , 1996 , 1 : 2435 —2437
[58] Singh J , Ator M A , Jaeger E P , Allen M P , Whipple D A , Soloweij J E , Chowdhary S , Treasurywala A M. J . Am. Chem. Soc. ,1996 , 118 : 1669 —1676
[59] Brown R D , Martin Y C. J . Med. Chem. , 1997 , 40 : 2304 —2313
[60] Tomandl D , Schober A , Schwienhorst A. Journal of Computer Aided Molecular Design , 1997 , 11 : 29 —38
[61] Gillet V J , Willett P , Bradshaw J . J . Chem. Inf . Comp. Sci . ,1997 , 37 : 731 —740
[62] Gobbi A , Poppinger D. Biotechnol . Bioeng. , 1998 , 61 : 47 —54
[63] Weber L. Drug Discovery Today , 1998 , 3 : 379 —385
[64] Brown R D , Clark D E. Expert Opin. Ther. Pat . , 1998 , 8 :1447 —1459
[65] Tominaga Y. Chemometrics and Intelligent Laboratory Systems ,1998 , 43 : 157 —163
[66] Tominaga Y. Journal of Chemical Information and Computer Sciences , 1998 , 38 : 867 —875
[67] Gobbi A , Poppinger D. Biotechnol . Bioeng. , 1998 , 61 : 47 —53
[68] Gillet V J , Willett P , Bradshaw J , Green D V S. Journal of Chemical Information and Computer Sciences , 1999 , 39 : 169 —177
[69] Reynolds C H. J . Comb. Chem. , 1999 , 1 : 297 —306
[70] Bravi G, Green D V S , Hann M M, Leach A R. J . Chem. Inf .Comput . Sci . , 2000 , 40 : 1441 —1448
[71] Gillet V J , Khatib W, Willett P , Fleming P J , Green D V S. J .Chem. Inf . Comp. Sci . , 2002 , 42 : 375 —385

[1] Guizhao Liang1,Hu Mei1,Yuan Zhou1,Zhiliang Li 1,2*. Modeling Techniques of Multidimensional Quantitative Structure-Activity Relationship in Computer-Aided Drug Design [J]. Progress in Chemistry, 2006, 18(01): 120-130.
[2] Hou Tingjun,Xu Xiaojie**. Recent Progress in Comparative Molecular Field Analysis [J]. Progress in Chemistry, 2001, 13(06): 436-.
[3] He Xianf eng,Zhou Jiaju. Genetic Algorithms and Their Applications in Chemistry and Chemical Engineering [J]. Progress in Chemistry, 1998, 10(03): 312-.
[4] Zhao Shanrong,Jiang Hualiang,Liu Dongxiang,Chen Kaixian. Genetic Algorithm and Drug Molecular Design [J]. Progress in Chemistry, 1997, 9(04): 405-.