Article citationsMore>>
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:
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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.
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