Inhibitor peptide design for NF- KB: Markov model & genetic algorithm

2010 5th International Symposium on Health Informatics and Bioinformatics, HIBIT 2010

Volumn , Issue , 2010, Pages 72-80

  Besray Unal, E ^a   Gursoy, Attila ^a   Erman, Burak ^a  

^a KOÇ UNIVERSITY   (Turkey)

Author keywords

Genetic algorithm; Inhibitor; Markov model; Nf b; Peptide design

Indexed keywords

AUTODOCK; BINDING PEPTIDE; BLOCK ACTIVITY; DI-PEPTIDES; MARKOV CHAIN; MARKOV MODEL; NATURAL AMINO ACIDS; PEPTIDE DESIGN; PEPTIDE SEQUENCES; PROBABILISTIC METHODS; STATISTICAL WEIGHT; TARGET PROTEINS; TOURNAMENT SELECTION;

AMINO ACIDS; BINDING ENERGY; BIOINFORMATICS; CHROMOSOMES; DESIGN; HEURISTIC METHODS; MARKOV PROCESSES; ORGANIC ACIDS; PEPTIDES; THERMODYNAMIC PROPERTIES;

GENETIC ALGORITHMS;

EID: 77954480377     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/HIBIT.2010.5478904     Document Type: Conference Paper

References (26)

1. Abe K. et al., "Peptide ligand screening of a-synuclein aggregation modulators bu in silico panning," BMC Bioinformatics, vol.8, pp. 451,2007. (Pubitemid 351256321)
2. Belda I. et al., "ENPDA: an evolutionary structure-based de novo peptide design algorithm," Journal of Computer-Aided Molecular Design, vol. 19, pp. 585-601,2005. (Pubitemid 43150050)
3. Hanai T. et al., "Computational Design of Proteinous Drug Employing Hidden Markov Model," Genome Informatics, vol. 11, pp. 394-395, 2000.
4. Kato R. et al., "Hidden Markov model-based approach as the first screening of binding peptides that interact with MHC class II molecules," Enzyme and Microbial Technology, vol. 33, pp. 472-481,2003. (Pubitemid 37011398)
5. Noguchi H. et al., "Hidden Markov Model-Based Prediction of Antigenic Peptides That Interact with MHC Class II Molecules," Journal of Bioscience and Bioengineering, vol. 94(3), pp. 264-270, 2003.
6. Unal E.B., Gursoy A., Erman B., "Conformational energies and entropies of peptides, and the peptide-protein binding problem," Physical Biology, vol. 6, pp. 036014,2009.
7. Holland J.H. "Adaptation in natural and artificial systems," MIT Press, Cambridge, MA, 1992.
8. Kamphausen S. et al., "Genetic Algorithm for the Design of Molecules with Desired Properties," J. Comp.-Aided Mol. Des., vol. 16, pp. 551,2002.
9. Morris G.M. et al., "Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function," J. Computational Chemistry, vol. 19, pp. 1639,1998.
10. Goldberg D.E., Deb K. "Foundations of Genetic Algorithms. San Mateo, California," USA: Morgan Kaufmann Publishers, pp. 69-93, 1991.
11. Michalewicz Z., "Genetic Algorithms + Data Structures = Evolution Programs," Springer, 1992.
12. Grinstead C.M., Snell J.L., "Introduction to Probability1, American Mathematical Society, 1997.
13. Rabiner L.R., "A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition," Proceedings of the IEEE, vol. 77(2), pp. 257-286, 1989.
14. Bystroff CA. et al., "Hidden Markov Models for Prediction of Protein Features," Methods in Molecular Biology, vol. 413, pp. 173-198, 2008.
15. Sramek R., Brejova B., Vinar T., "On-line Viterbi Algorithm for Analysis of Long Biological Sequences," Algorithms in Bioinformatics, 7th International Workshop, WABI 2007, Philadelphia, PA, USA: Springer, 2007.
16. Mirabeau O. et al., "Identification of novel peptide hormones in the human proteome by Hidden Markov model screening," Genome Research, vol. 17, pp. 320-327, 2007.
17. Haliloglu T. and Erman B., "Analysis of Correlations between Energy and Residue Fluctuations in Native Proteins and Determnation of Specific Sites for Binding," Physical Review Letters, vol. 102(8), pp. 088103, 2009.
18. Haliloglu T., Seyrek E., and Erman B., "Prediction of Binding Sites in Receptor-Ligand Complexes with the Gaussian Network Model," Physical Review Letters, vol. 100(22), pp. 228102, 2008.
19. Jones G., Willett P. and Glen R.C., "Evolutionary and genetic methods in drug design," J. Mol. Biol., vol. 245, pp. 43, 1995.
20. Huxford T., Ghosh G., "A Structural Guide to Proteins of the NFkappaB Signaling Module," Cold Spring Harbor Perspect Biol., vol. 1(3): a000075, 2009.
21. Huxford T. et al., "The Crystal Structure of the IkappaBalpha/NFkappaB Complex Reveals mechanisms of NF-kappaB inactivation," Cell, vol. 95, pp.759,1998.
22. Humphrey W., Dalke A., and Schulten F., "VMD - Visual Molecular Dynamics," J. Molec. Graphics, vol. 14, pp. 33-38, 1996.
23. HyperChem(TM) Professional 7.51, Hypercube, Inc., 1115 NW 4th Street, Gainesville, Florida 32601, USA.
24. Flory P.J., "Statistical Mechanics of Chain Molecules," New York: Wiley, 1969.
25. Joliot A., "Antennapedia homeobox peptide regulates neural morphogenesis," Proc. Natl. Acad. Sci. USA, vol. 88, pp. 1864-1868, 1991.
26. DS Modeling 2.5, Accelrys Inc.