Optimal HP configurations of proteins by combining local search with elastic net algorithm

Journal of Biochemical and Biophysical Methods

Volumn 70, Issue 3, 2007, Pages 335-340

  Guo, Yu Zhen ^a   Feng, En Min ^a   Wang, Yong ^b,c  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c OSAKA SANGYO UNIVERSITY   (Japan)

Author keywords

2D HP lattice model; Elastic net algorithm; Local search method; Protein folding problem

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; ENERGY; HYDROPHOBICITY; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING;

ALGORITHMS; BIOPHYSICS; ELASTICITY; HYDROPHOBICITY; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 33847636089     PISSN: 0165022X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbbm.2006.08.001     Document Type: Article

References (21)

1. Zhen-Ping, Li. Combinatorial optimization problems in bioinformatics. PhD thesis. Institute of Applied Mathematics, Academy of Mathematics and System Sciences, CAS, Beijing, 2004.
2. Hayes B. Proteins. Am Sci 86 (1999) 216-221
3. Anfinsen C.B. Principles that govern the folding of protein chains. Science 181 (1973) 223-230
4. Jiang T.-Z., Cui Q.-H., Shi G.-H., and Ma S.-D. Protein folding simulations of the hydrophilic model by combining tabu search with genetic algorithms. J Chem Phys 119 8 (2003) 4592-4596
5. Liang F.-M., and Wong W.H. Evolutionary Monte Carlo for protein folding simulations. J Chem Phys 115 7 (2001) 3374-3380
6. Zhang X.-S., Wang Y., Zhan Z.-W., Wu L.-Y., and Chen L.-N. Exploring protein's optimal HP configurations by self-organizing. J Bioinf Comput Biol 3 2 (2005) 385-400
7. Wang Y., Zhan Z.-W., Wu L., and Zhang X.-S. An improved self organizing map algorithm for protein folding and its realization. J Syst Sci Math Sci 25 1 (2004) 1-12
8. Zou Z. Application of guided simulated annealing method on analysis of protein structure. Proseminar of some problems about analysis of protein structure (2002)
9. Shmygelska A., Hernández R.A., and Hoos H.H. An ant colony optimization algorithm for the 2D HP protein folding problem. Ant Algorithms (2002) 40-53
10. Lin S., and Kernighan B. An effective heuristic algorithm for the travelling salesman problem. Oper Res 21 (1973) 498-516
11. Hopfield J.J., and Tank D.W. Neural computation of decisions in optimization problems. Biol Cybern 52 (1985) 141-152
12. Miller D.L., and Pekny J.F. Exact solution of large asymmetric travelling salesman problem. Science 251 (1991) 754-761
13. Potvin J.Y. The travelling salesman problem: a neural network perspective. ORSA J Comput 203 5 (1993) 328-348
14. Budinich M. A self-organizing neural network for the travelling salesman problem that is competitive with simulated annealing. Neural Comput 8 2 (1996) 416-424
15. Durbin R., and Willshaw D. An analogue approach to the travelling salesman problem using an elastic net method. Nature 326 (1987) 689-691
16. Dill K.A. Theory for the folding and stability of globular proteins. Biochemistry 24 6 (1985) 1501-1509
17. Krasnogor N., Hart W.E., Smith J., and Pelta D.A. Protein structure prediction with evolutionary algorithms. Proceedings of the genetic and evolutionary computation conference (1999)
18. Ball K.D., Erman B., and Dill K.A. The elastic net algorithm and protein structure prediction. J Comput Chem 23 1 (2002) 77-83
19. Yanikoglu B., and Erman B. Minimum energy configurations of the 2-dimensional HP-model of proteins by self-organizing networks. J Comput Biol 9 4 (2002) 613-620
20. Willian Hart, Sorin Istrail:http://www.cs.sandia.gov/tech_reports/compbil/tortilla-hp-benchmarks.html.
21. Durbin R., Szeliski R., and Yuille A. An analysis of the elastic net approach to the travelling salesman problem. Neural Comput 1 3 (1989) 348-358