Employing reduced order approach for computing protein folding via Langevin equation and Lyapunov theorem

International Journal of Innovative Computing, Information and Control

Volumn 8, Issue 6, 2012, Pages 4319-4332

  Sung, Wen Tsai ^a   Chung, Hung Yuan ^b  

^a NATIONAL CHIN YI UNIVERSITY OF TECHNOLOGY   (Taiwan)

^b NATIONAL CENTRAL UNIVERSITY   (Taiwan)

Author keywords

Drug docking; Minimum energy; Molecular visualization; Protein folding

Indexed keywords

COMPUTATION MODEL; DISTANCE MATRICES; FORCE FIELDS; LANGEVIN EQUATION; LOCAL MINIMUMS; LYAPUNOV THEOREMS; MINIMUM ENERGY; MOLECULAR DOCKING; MOLECULAR ORDERS; MOLECULAR VISUALIZATION; NP COMPLETE; REDUCED ORDER; SCORING FUNCTIONS; STRUCTURE COMPUTATION;

ALGORITHMS; DIFFERENTIAL EQUATIONS; MOLECULAR STRUCTURE; PROTEIN FOLDING; VISUALIZATION;

THEOREM PROVING;

EID: 84861382390     PISSN: 13494198     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (23)

1. M. G. B. Drew, G. R. H. Wilden, W. J. Spillane, R. M. Walsh, C. A. Ryder and J. M. Simmie, Quantitative structure-activity relationship studies of sulfamates RNHS03Na: Distinction between sweet, sweet-bitter, and bitter molecules, J. Agric. Food Chem., vol.46, pp.3016-3026, 1998.
2. M. G. Albuquerque, A. J. Hopfinger, E. J. Barriero and R. B. Alencastro, Four dimensional quantitative structure-activity relationship analysis of a series of interphenylene 7-oxabicycloheptane oxazole thromboxane A2 receptor antagonists, Journal of Chemical Information and Computer Sciences, vol.38, pp.925-938, 1998.
3. Y. Tominaga, Novel 3-D descriptors using excluded volume 2: Application to drug classification, Journal of Chemical Information and Computer Sciences, vol.38, pp.1157-1160, 1998.
4. C.-C. Tsai, S.-C. Ou, C.-Y. Chung, W.-T. Sung, C.-C. Chien and D.-Y. Su, Predict protein structure and similar function via 3D visualization tools-case study of bamboo shoot, International Proteomics Conference, Taipei, Taiwan, 2004.
5. W.-T. Sung, J.-H. Chen, M.-H. Wang and Y.-C. Hsu, Remote medical care system design based on RFID and zigbee technology via wireless sensors network, International Journal of Innovative Computing, Information and Control, vol.6, no.11, pp.5203-5220, 2010.
6. S.-C. Ou, C.-Y. Chung, W.-T. Sung, C.-C. Tsai, C.-C. Chien and D.-Y. Su, Virtual screening and computer-aided drug design in molecular docking via lyapunov function, WSEAS Trans, on Biology and Biomedicine, vol.01, no.4, pp.384-390, 2004.
7. J. R. Ullman, An algorithm for subgraph isomorphism, J. Assoc. Comput. Mach., vol.23, no. 1, pp.31-42, 1976.
8. S.-J. Hsiao, W.-T. Sung and S.-C. Ou, Web-based search system of pattern recognition for the pattern of industrial component by an innovative technology, Computer in Industry Journal, vol.53, no.2, pp.179-192, 2004.
9. W.-T. Sung and S.-C. Ou, Using virtual reality technologies for manufacturing applications, International Journal of Computer Applications in Technology, vol.17, no.4, pp.213-219, 2003.
10. J.-M. Yang and C.-Y. Kao, Flexible ligand docking using a robust evolutionary algorithm, J. Comput. Chem., vol.21, pp.988-998, 2000.
11. E. D. H. Wolpert and W. G. Macready, No free lunch theorems for optimization, IEEE Trans, on Evolutionary Computation, vol.1, pp.67-82, 1997.
12. W.-T. Sung and S.-C. Ou, Integrating network, CAD and VR into the design and development of web-based computer graphics learning materials, Journal of Computer Science, vol.14, no.2, pp.47-63, 2001.
13. E. C. Meng, B. K. Shoichet and I. D. Kuntz, Automated docking with grid-based energy evaluation, J. Comput. Chem., vol.13, pp.505-524, 1998.
14. A. Vedani, M. Dobler and P. Zbinden, Quasi-atomistic receptor surface models: A bridge between 3-D QSAR and receptor modeling, Journal of the American Chemical Society, vol.120, pp.4471-4477, 1998.
15. D. Levine, M. Facello, P. Hallstrom, G. Reeder, B. Walenz and F. Stevens, STALK: An interactive system for virtual molecular docking, IEEE Comput. Sci. Eng., vol.4, pp.55-65, 1997.
16. R. J. Davy and I. A. Hiskens, Lyapunov functions for multi-machine power systems with dynamic loads, IEEE Trans, on Circuits and Systems, vol.23, no.4, pp.167-173, 1994.
17. W.-T. Sung and Y.-F. Liu, Energy minimum theorem based on AGA, Lyapunov and Force Field for CADD Techniques, Computers in Biology and Medicine, vol.40, no.2, pp.215-222, 2010.
18. W.-T. Sung and Y.-C. Hsu, Designing an industrial real-time measurement and monitoring system based on embedded system and ZigBee, Expert Systems with Applications, vol.38, no.4, pp.4522-4529, 2011.
19. Z. B. Musa and J. Watada, A particle filter approach for multi-camera tracking systems in a large view space, International Journal of Innovative Computing, Information and Control, vol.6, no.6, pp.2827-2836, 2010.
20. V. Kalashnikov, F. Camacho and R. A. N. Kalashnykova, Comparison of algorithms for solving a bi-level toll setting problem, International Journal of Innovative Computing, Information and Control, vol.6, no.8, pp.3529-3550, 2010.
21. K. Yoshida and Y. Nishizawa, Bifurcation analysis of noise-induced synchronization, International Journal of Innovative Computing, Information and Control, vol.5, no.9, pp.2809-2818, 2009.
22. H. Nakano, A. Utani, A. Miyauchi and H. Yamamoto, Chaos synchronization-based data transmission scheme in multiple sink wireless sensor networks, International Journal of Innovative Computing, Information and Control, vol.7, no.4, pp.1983-1994, 2011.
23. W.-T. Sung, H.-Y. Chung, Y.-C. Hsu and K.-Y. Chen, A light wind speed measurement system design to strengthen wireless sensor network functions, International Journal of Innovative Computing, Information and Control, vol.7, no.2, pp.859-868, 2011.