Please use this identifier to cite or link to this item:
http://hdl.handle.net/10397/6966
DC Field | Value | Language |
---|---|---|
dc.contributor | Department of Applied Mathematics | - |
dc.creator | Zhang, J | - |
dc.creator | Hou, Y | - |
dc.creator | Wang, Y | - |
dc.creator | Wang, C | - |
dc.creator | Zhang, X | - |
dc.date.accessioned | 2014-12-11T08:29:18Z | - |
dc.date.available | 2014-12-11T08:29:18Z | - |
dc.identifier.issn | 2150-4091 (print) | - |
dc.identifier.issn | 2150-4105 (online) | - |
dc.identifier.uri | http://hdl.handle.net/10397/6966 | - |
dc.language.iso | en | en_US |
dc.publisher | Scientific Research | en_US |
dc.rights | Copyright © 2012 SciRes. | en_US |
dc.rights | This is an open access article distributed under the Creative Commons License. | en_US |
dc.rights | 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 http://dx.doi.org/10.4236/ns.2012.412A138 | en_US |
dc.subject | Protein 3D structure | en_US |
dc.subject | Computational approaches | en_US |
dc.subject | Optimization method | en_US |
dc.subject | Molecular modelling | en_US |
dc.subject | Prion AGAAAAGA amyloid fibrils | en_US |
dc.title | The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils | en_US |
dc.type | Journal/Magazine Article | en_US |
dc.identifier.spage | 1097 | - |
dc.identifier.epage | 1108 | - |
dc.identifier.volume | 4 | - |
dc.identifier.issue | 12A | - |
dc.identifier.doi | 10.4236/ns.2012.412A138 | - |
dcterms.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. | - |
dcterms.accessRights | open access | en_US |
dcterms.bibliographicCitation | Natural science, Dec. 2012, v. 4, no. 12A, p. 1097-1108 | - |
dcterms.isPartOf | Natural science | - |
dcterms.issued | 2012-12 | - |
dc.description.oa | Version of Record | en_US |
dc.identifier.FolderNumber | OA_IR/PIRA | en_US |
dc.description.pubStatus | Published | en_US |
Appears in Collections: | Journal/Magazine Article |
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File | Description | Size | Format | |
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Zhang_LBFGS_quasi_newtonian.pdf | 1.07 MB | Adobe PDF | View/Open |
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