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Title: The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils
Authors: Zhang, J
Hou, Y
Wang, Y
Wang, C
Zhang, X
Keywords: Protein 3D structure
Computational approaches
Optimization method
Molecular modelling
Prion AGAAAAGA amyloid fibrils
Issue Date: Dec-2012
Publisher: Scientific Research
Source: Natural science, Dec. 2012, v. 4, no. 12A, p. 1097-1108 How to cite?
Journal: Natural science 
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.
ISSN: 2150-4091 (print)
2150-4105 (online)
DOI: 10.4236/ns.2012.412A138
Rights: Copyright © 2012 SciRes.
This is an open access article distributed under the Creative Commons License.
The article: Zhang, J., Hou, Y., Wang, Y., Wang, C., & Zhang, X. (2012). The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils. Natural science, 4(12A), p. 1097-1108 is available at
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