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Case, D.A., Darden, T.A., Cheatham, T.E., Simmerling III, C.L., Wang, J., Duke, R.E., Luo, R., Walker, R.C., Zhang, W., Merz, K.M., Roberts, B.P., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kolossvary, I., Wong, K.F., Paesani, F., Vanicek, J., Liu, J., Wu, X., Brozell, S.R., Steinbrecher, T., Gohlke, H., Cai, Q., Ye, X., Wang, J., Hsieh, M.-J., Cui, G., Roe, D.R., Mathews, D.H., Seetin, M.G., Sagui, C., Babin, V., Luchko, T., Gusarov, S., Kovalenko, A. and Kollman, P.A. (2010) AMBER 11. University of California, San Francisco.

has been cited by the following article:

• TITLE: The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils

  AUTHORS: Jiapu Zhang, Yating Hou, Yiju Wang, Changyu Wang, Xiangsun Zhang

  KEYWORDS: Protein 3D Structure; Computational Approaches; Optimization Method; Molecular Modelling; Prion AGAAAAGA Amyloid Fibrils

  JOURNAL NAME: Natural Science, Vol.4 No.12A, December 31, 2012

  ABSTRACT: Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein); theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.