C. M. Oshiro, I. D. Kuntz, and J. S. Dixon. Flexible ligand docking using a genetic algorithm. Journal of Computer-Aided Molecular Design, 9(2):113-130, 1995.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....algorithm, global optimization, local optimization, fast Fourier transforms. 1 Introduction Computer technology has revolutionized the way drugs are designed and analyzed. Not only do reliable methods for docking prediction exist, but there are a multitude of good techniques available (cf: [1, 6, 7, 8, 11, 13, 14, 17, 19, 20, 22, 26, 29, 35, 37, 38]. The CASP2 docking assessment compared a number of distinct techniques for studying protein interactions [4] The quality of submitted structures was quite good on the whole, and no method stood out as being exceptional in comparison with the others. Accuracy and speed are both important ....

Oshiro, C.M., Kuntz, I.D. and Dixon, J.S. (1995), "Flexible ligand docking using a genetic algorithm," Journal of Computer Aided Molecular Design, Vol. 9, No. 2, 113-30. 15

....algorithms have been developed for studying and predicting protein protein and protein ligand Copyright 1999, American Association for Artificial Intelligence (www.aaai.org) All rights reserved. interactions [Kuntz et al. 1982; Shoichet and Kuntz, 1993; Leach, 1994; Fisher et al. 1995; Oshiro et al. 1995; Lengauer and Rarey, 1996; Rarey et al. 1996; Sobolev et al. 1996; Gabb et al. 1997; Jones et al. 1997; Lenhof, 1997; Morris et al. 1998] In the case of protein protein binding, algorithms have been developed to predict the contact surfaces involved in the interaction and the conformation ....

Oshiro, C. M., Kuntz, I. D. and Dixon, J. S. (1995). Flexible ligand docking using a genetic algorithm. J Comput Aided Mol Des, 9(2), 113-30.

....as diverse as geographical data analysis and molecular modelling deal with location as a special feature within a vector of attributes that describe a problem. Generic GAs have been used in applications such as electronic engineering design problems [6] molecular conformational analysis [13,14, ; network and graph optimisation [15,17] These systems deal with a variety of graph based representations but typically use a one dimensional encoding which means that either spatial information is lost, or extra, problem specific constraints have to be introduced. Hybrid GAs which model the ....

C.M. Oshiro, I.D. Kuntz and J. Scott Dixon. Flexible ligand docking using a genetic algorithm. Journal of Computer-Aided Molecular Design, 9:113-130. 1993.

.... [151] IEE Proceedings, Vision, Image, Signal Processing, 66] IEEE Transactions on Power Systems, 22] International Journal of Approximative Reasoning, 196] International Journal of Intelligent Systems, 286] Journal of Chemical Physics, 97] Journal of Computer Aided Molecular Design, [46] Journal of Molecular Biology, 106] Knowledge and Information Systems. An International Journal, 137] Lettre du Transputer et des Calculateurs Distribu es, 418] Machine Learning, 361] Mathware Soft Computing, 241] Molecular Simulations, 125] Neural Computing and Applications, 409] ....

....N. 158, 172, 44, 212, 236, 94] Konstam, Aaron H. 386] Koskim aki, Esa, 262] Kov acs, Attila, 79] 16 Genetic algorithms available via ftp and www Krasnogor, Natalio, 133] Krejsa, Ji r , 316] Kreutz, Martin, 49] Krishnamoorthy, M. 343] Kuhn, Leslie A. 74, 106] Kuntz, I. D. [46] Kuosmanen, Pauli, 199] Ku s cu, Ibrahim, 165] Kuvayev, L. 310] Kyng as, Jari, 263] Kyuma, Kazuo, 348] Lahdelma, Risto, 204, 214] Lahtinen, Jussi, 264] Lampinen, Jouni, 282, 294, 325] Langdon, William Benjamin, 278] Lanitis, A. 45] Laurikkala, Jorma, 326] Lee, Terry, ....

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C. M. Oshiro, I. D. Kuntz, and J. Scott Dixon. Flexible ligand docking using a genetic algorithm. Journal of Computer-Aided Molecular Design, 9(2):113-130, April 1995. Key: ga95aOshiro.

.... [109] IEE Proceedings, Vision, Image, Signal Processing, 47] IEEE Transactions on Power Systems, 21] International Journal of Approximative Reasoning, 155] International Journal of Intelligent Systems, 246] Journal of Chemical Physics, 75] Journal of Computer Aided Molecular Design, [36] Journal of Molecular Biology, 84] Lettre du Transputer et des Calculateurs Distribu es, 373] Machine Learning, 316] Mathware Soft Computing, 201] Molecular Simulations, 96] Neural Computing and Applications, 364] Nucleic Acids Research, 54] Pattern Recognition Letters, 42] ....

....Hannu, 227] Koivisto, Pertti, 158] Koivo, Heikki N. 217, 264] Kok, Joost N. 116, 131, 34, 172, 196, 72] Konstam, Aaron H. 341] Koskimaki, Esa, 222] Kov acs, Attila, 60] Krejsa, Jir i, 276] Kreutz, Martin, 38] Krishnamoorthy, M. 298] Kuhn, Leslie A. 55, 84] Kuntz, I. D. [36] Kuosmanen, Pauli, 158] Kuscu, Ibrahim, 123] Kuvayev, L. 270] Kyngas, Jari, 223] Kyuma, Kazuo, 303] Lahdelma, Risto, 163, 174] Lahtinen, Jussi, 224] Lampinen, Jouni, 242, 254, 284] Langdon, William Benjamin, 238] Lanitis, A. 35] Laurikkala, Jorma, 285] Lee, Terry, 39] ....

[Article contains additional citation context not shown here]

C. M. Oshiro, I. D. Kuntz, and J. Scott Dixon. Flexible ligand docking using a genetic algorithm. Journal of Computer-Aided Molecular Design, 9(2):113--130, April 1995. Key: ga95aOshiro.

.... Journal of Chemical Technology and Biotechnology, 58] Journal of Chemometrics, 299] Journal of Computational Chemistry, 37, 40, 48, 49, 51, 968, 994, 65, 1007, 1121, 1166, 68, 81, 101, 102, 1109] Journal of Computer and System Sciences, 610] Journal of Computer Aided Molecular Design, [271, 272, 965, 1150, 1153, 1022, 1174, 197] Journal of General Virology, 435] Journal of Geomagnetism and Geoelectricity, 560] Journal of Global Optimization, 412] Journal of Japanese Society for Arti cial Intelligence, 625] Journal of Magnetic Resonance, 407, 1136] Journal of Magnetic Resonance (Series B) 1158] Journal of ....

....Laurent, 537] Kr ahenb uhl, L. 811, 515] Kral, J. 825] Kramer, M. 71] Krasnogor, Natalio, 911, 1043, 1062] Krause, Je rey L. 868] Krogh, A. 950] Kubinyi, H. 930, 942, 299] Kuhn, Leslie A. 300, 998, 1173] Kulkarni, Bhaskar D. 199] Kumskov, K. I. 327] Kuntz, I. D. [965] Kuntz, P. J. 409, 410, 411] Kunze, M. 832] Kusuma, Tony, 566] Kuzmicz, W. 849] Kuznetsov, Alex V. 868] Kyng as, J. 314] Lakner, R. 309] Lamont, Gary B. 933, 956] Landman, Uzi, 361] Landree, E. 434] Landweber, Laura F. 629] Lane, R. 137] Lang, M. J. 786] Lange, ....

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C. M. Oshiro, I. D. Kuntz, and J. Scott Dixon. Flexible ligand docking using a genetic algorithm. Journal of Computer-Aided Molecular Design, 9(2):113-130, April 1995. ga95aOshiro.

....on both rigid receptor and ligand conformations [64] more recent work has addressed the issue of flexible ligand docking [65] In a similar way, genetic algorithms have recently been used to dock flexible ligands. In some cases, scoring functions have been based on potential energy force fields [137], although some modified potentials have also been used [73] The results of one method [76] which includes solvation effects, have emphasized the need for developing reliable scoring functions. In general, as with simulated annealing, the ability to model flexibility is limited as ligand size ....

C. M. Oshiro, I. D. Kuntz and J. S. Dixon, Flexible ligand docking using a genetic algorithm, J. Comput. Aided Mol. Design, 9, (1995), 113-130. GLOBAL OPTIMIZATION IN PROTEIN FOLDING AND PEPTIDE DOCKING 29

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C. M. Oshiro, I. D. Kuntz, and J. S. Dixon. Flexible ligand docking using a genetic algorithm. Journal of Computer-Aided Molecular Design, 9(2):113-130, 1995.

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Oshiro C, Kuntz I, Dixon J. Flexible ligand docking using a genetic algorithm. J Comput Aided Mol Des 1995;9:113--130.

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