A multi-objective optimization energy approach to predict the ligand conformation in a docking process

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7831 LNCS, Issue , 2013, Pages 181-192

  Sandoval Perez, Angelica ^a,b   Becerra, David ^a,c   Vanegas, Diana ^a   Restrepo Montoya, Daniel ^a   Nino, Fernando ^a  

^a UNIVERSIDAD NACIONAL DE COLOMBIA   (Colombia)

^b UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

^c MCGILL UNIVERSITY   (Canada)

Author keywords

bonding and non bonding energy terms; MOEA; rotatable bonds

Indexed keywords

CONFORMATION AND CONFIGURATION; CONFORMATIONAL SPACE; ENERGY CONTRIBUTION; LIGAND CONFORMATIONS; MOEA; MULTI OBJECTIVE EVOLUTIONARY ALGORITHMS; RECEPTOR-LIGAND COMPLEX; ROTATABLE BONDS;

COMPLEXATION; FORECASTING; GENETIC PROGRAMMING; MOLECULAR INTERACTIONS; MOLECULAR STRUCTURE; MULTIOBJECTIVE OPTIMIZATION; PARETO PRINCIPLE;

LIGANDS;

EID: 84875119065     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-37207-0_16     Document Type: Conference Paper

References (26)

1. Branke, J., Deb, K., Dierolf, H., Osswald, M.: Finding Knees in Multi-objective Optimization. In: Yao, X., Burke, E.K., Lozano, J.A., Smith, J., Merelo-Guervós, J.J., Bullinaria, J.A., Rowe, J.E., Tiňo, P., Kabán, A., Schwefel, H.-P. (eds.) PPSN 2004. LNCS, vol. 3242, pp. 722-731. Springer, Heidelberg (2004), http://citeseerx.ist.psu.edu/viewdoc/ summary?doi=10.1.1.76.9689
2. Brooijmans, N., Kuntz, I.D.: Molecular recognition and docking algorithms. Annu. Rev. Biophys. Biomol. Struct. 32, 335-373 (2003)
3. Brünger, A.T., Leahy, D.J., Hynes, T.R., Fox, R.O.: The 2.9 Å resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody fab fragment with bound hapten. J. Mol. Biol. 221(1), 239-256 (1991)
4. Case, D., Darden, T., Cheatham Iii, T., Simmerling, C., Wang, J., Duke, R., Luo, R., Crowley, M., Walker, R., Zhang, W., et al.: Amber 10, vol. 32. University of California, San Francisco (2008)
5. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., Kollman, P.: A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. JACS 117(19), 5179-5197 (1995), http://dx.doi.org/10.1021/ ja00124a002
6. Deb, K., Pratap, A., Agarwal, S., Meyarivan, T.: A fast and elitist multiobjective genetic algorithm: Nsga-ii. IEEE Transactions on Evolutionary Computation 6(2), 182-197 (2002)
7. Dehuri, S., Cho, S.B.: Multi-criterion pareto based particle swarm optimized polynomial neural network for classification: A review and state-of-the-art. Comp. Sci. Rev. 3(1), 19-40 (2009)
8. Dong, Q., Wu, Z.: A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances. J. Global Opt. 22(1), 365-375 (2002), http://dx.doi.org/10.1023/A:1013857218127
9. Durillo, J., Nebro, A., Luna, F., Dorronsoro, B., Alba, E.: jmetal: a java framework for developing multi-objective optimization metaheuristics. Departamento de Lenguajes y Ciencias de la Computación, University of Málaga, ETSI Informática, Campus de Teatinos, Tech. Rep. ITI-2006-10 (2006)
10. Hanser, T., Jauffret, P., Kaufmann, G.: A new algorithm for exhaustive ring perception in a molecular graph. J. Chem. Inf. Comput. Sci. 36(6), 1146-1152 (1996)
11. Ishida, M., Asakura, T., Yokoi, M., Saito, H.: Solvent-and mechanical-treatment-induced conformational transition of silk fibroins studies by high-resolution solid-state carbon-13 nmr spectroscopy. Macromolecules 23(1), 88-94 (1990)
12. Jones, G., Willett, P., Glen, R.C., Leach, A.R., Taylor, R.: Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267(3), 727-748 (1997), http://view.ncbi.nlm.nih.gov/pubmed/9126849
13. Kapetanovic, I.M.: Computer-aided drug discovery and development (caddd): in silico-chemico-biological approach. Chemico-Biological Interact. 171(2), 165-176 (2008)
14. Kramer, B., Rarey, M., Lengauer, T.: Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins 37(2), 228-241 (1999), http://dx.doi.org/10.1002/(SICI)1097-0134(19991101)37:2〈228::AID- PROT8〉3.0.CO;2-8
15. Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R., Ferrin, T.E.: A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161(2), 269-288 (1982)
16. Lawson, C.L., Van Montfort, R., Strokopytov, B., Rozeboom, H., Kalk, K., de Vries, G., Penninga, D., Dijkhuizen, L., Dijkstra, B.W.: Nucleotide sequence and X-ray structure of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 in a maltose-dependent crystal form. J. Mol. Biol. 236(2), 590-600 (1994)
17. Lepre, C.A., Moore, J.M., Peng, J.W.: Theory and applications of nmr-based screening in pharmaceutical research. Chem. Rev. 104(8), 3641-3676 (2004)
18. Lodish, H., Baltimore, D., Berk, A., Darnell, J.: Molecular cell biology. WH Freeman, New York (1995)
19. Makino, S., Kuntz, I.D.: Automated flexible ligand docking method and its application for database search. J. Comp. Chem. 18(14), 1812-1825 (1997)
20. Moustakas, D., Lang, P., Pegg, S., Pettersen, E., Kuntz, I.D., Brooijmans, N., Rizzo, R.: Development and validation of a modular, extensible docking program: DOCK5. J. Comput. Aided Mol. Des. 20, 601-619 (2006), http://dx.doi.org/10.1007/s10822-006-9060-4, doi:10.1007/s10822-006-9060-4
21. Nicolaou, C.A., Brown, N., Pattichis, C.S.: Molecular optimization using computational multi-objective methods. Curr. Opin. Drug Discov. Dev. 10(3), 316 (2007)
22. Quiocho, F.A., Vyas, N.K.: Novel stereospecificity of the l-arabinose-binding protein. Nature 310(5976), 381-386 (1984)
23. Sams-Dodd, F.: Target-based drug discovery: is something wrong? Drug Discov. Today 10(2), 139-147 (2005)
24. Stebbins, J., Robertson, D., Roberts, M., Stevens, R., Lipscomb, W., Kantrowitz, E.: Arginine 54 in the active site of Escherichia coli aspartate transcarbamoylase is critical for catalysis: A site-specific mutagenesis, nmr, and x-ray crystallographic study. Prot. Sci. 1(11), 1435-1446 (2008)
25. Subasi, E., Basdogan, C.: A new haptic interaction and visualization approach for rigid molecular docking in virtual environments. Presence 17(1), 73-90 (2008)
26. Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., Case, D.A.: Development and testing of a general amber force field. J. Comp. Chem. 25(9), 1157-1174 (2004)