Deterministic global optimization and torsion angle dynamics for molecular structure prediction

Computers and Chemical Engineering

Volumn 24, Issue 2-7, 2000, Pages 1761-1766

  Klepeis, J L ^a   Floudas, C A ^a  

^a Princeton University   (United States)

Author keywords

Global optimization; Molecular structure prediction; Torsion angle dynamics

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; OPTIMIZATION; PROTEINS;

GLOBAL OPTIMIZATION; TORSION ANGLE DYNAMICS;

MOLECULAR STRUCTURE;

ALGORITHM; CHEMICAL STRUCTURE; CONFERENCE PAPER; DATA ANALYSIS; DYNAMICS; MATHEMATICAL ANALYSIS; MOLECULE; PREDICTION; PROTEIN FOLDING;

EID: 0034661210     PISSN: 00981354     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0098-1354(00)00461-0     Document Type: Conference Paper

References (20)

1. Adjiman, C. S., Androulakis, I. P., & Floudas, C. A. (1998a). A global optimization method, αBB, for general twice-differentiable NLPs - II.: implementation and computational results. Computers and Chemical Engineering, 22, 1159-1179.
2. Adjiman, C. S., Dallwig, S., Floudas, C. A., & Neumaier, A. (1998b). A global optimization method, αBB, for general twice-differentiable NLPs - I.: theoretical advances. Computers and Chemical Engineering, 22, 1137-1158.
3. Androulakis, I. P., Maranas, C. D., & Floudas, C. A. (1995). αbb: a global optimization method for general constrained nonconvex problems. Journal of Global Optics, 7, 337-363.
4. Androulakis, I. P., Maranas, C. D., & Floudas, C. A. (1997). Global minimum potential energy conformation of oligopeptides. Journal of Global Optics, 11, 1-34.
5. Berendsen, H. J. C., Postina, J. P. M., van Gunsteren, W. R, DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81, 3684-3690.
6. Brünger, A. (1992). X-PLOR, version 3.1 a system for X-ray crystallography and NMR. New Haven, USA: Yak University Press.
7. Caves, L. S. D., Evanseck, J. D., & Karplus, M. (1998). Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin. Protein Science, 7, 649-666.
8. Duan, Y., & Kollman, P. A. (1998). Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science, 282, 740-744.
9. Floudas, C. A. (2000). Deterministic global optimization: theory, methods and applications; nonconvex optimization and its applications. Dordrecht: Kluwer.
10. Güntert, P., Mumenthaler, C., & Wüthrich, K. (1997). Torsion angle dynamics for NMR structure calculation with the new program dyana. Journal of Molecular Biology, 273, 283-298.
11. Jain, A., Vaidehi, N., & Rodriguez, G. (1993). A fast recursive algorithm for molecular dynamics simulation. Journal of Computational Physics, 106, 258-268.
12. Klepeis J. L., & Floudas C. A. (1999). A comparative study of global minimum energy conformations of solvated peptides. Journal of Computational Chemistry (in press).
13. Klepeis, J. L., Androulakis, I. P., Ierapetritou, M. G., & Floudas, C. A. (1998). Predicting solvated peptide conformations via global minimization of energetic atom-to-atom, interactions. Computers and Chemical Engineering, 22, 765-788.
14. Klepeis, J. L., Floudas, C. A., Morikis, D., & Lambris, J. D. (1999). Predicting peptide structures using nm data and deterministic global optimization. Journal of Computational Chemistry, 20, 1354-1370.
15. Maranas, C. D., Androulakis, I. P., & Floudas, C. A. (1996). DIMACS series in discrete mathematics and theoretical computer science. In A deterministic global optimization approach for the protein folding problem, vol. 23 (p. 133). American Mathematical Society.
16. Morikis, D., Assa-Munt, N., Sahu, A., & Lambris, J. D. (1998). Solution structure of compstatin, a potent complement inhibitor. Protein Science, 7, 619-627.
17. Némethy, G., Gibson, K. D., Palmer, K. A., Yoon, C. N., Paterlini, G., Zagari, A., Rumsey, S., & Scheraga, H. A. (1992). Energy parameters in polypeptides. 10. Journal of Physical Chemistry, 96, 6472.
18. Rice, L. M., & Brünger, A. T. (1994). Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins, 19, 277-290.
19. Sahu, A., Kay, B., & Lambris, J. (1996). Inhibition of human complement by a c3-binding peptide isolated from a phage-displayed random peptide library. Journal of Immunology, 157, 884-891.
20. Standley, D. M., Eyrich, V. A., Felts, A. K., Friesner, R. A., & McDermott, A. E. (1999). A branch and bound algorithm for protein structure refinement from sparse NMR data sets. Journal of Molecular Biology, 285, 1691-1710.