Global Convergence of a Special Case of the Dai–yuan Family Without Line Search

Zhu, Hui; Chen, Xiongda

doi:10.1142/s0217595908001663

Cited by 3 publications

(1 citation statement)

References 16 publications

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“…Here, we would like to use the hybrid local and global optimization search methods to investigate the optimal atomic-resolution amyloid fibril models in hopes that the findings thus obtained may be of use for controlling prion diseases. Using the traditional local search steepest descent and conjugate gradient [Li and Chen, 2005, Sun and Zhang, 2001, Zhu and Chen, 2008] methods hybridized with the standard global search simulated annealing method [Horst et al, 2003, Yiu et al, 2004, zhang (2011a) successfully constructed three optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils. These structures were constructed based on the breakthrough work of [Sawaya et al, 2007].…”

Section: Introductionmentioning

confidence: 99%

Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils

Zhang

Sun

2011

Journal of Theoretical Biology

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X-ray crystallography is a powerful tool to determine the protein 3D structure. However, it is time-consuming and expensive, and not all proteins can be successfully crystallized, particularly for membrane proteins. Although nuclear magnetic resonance (NMR) spectroscopy is indeed a very powerful tool in determining the 3D structures of membrane proteins, it is also time-consuming and costly. To the best of the authors' knowledge, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins due to the noncrystalline and insoluble nature of the amyloid fibril, although many experimental studies have shown that this region has amyloid fibril forming properties and plays an important role in prion diseases. In view of this, the present study is devoted to address this problem from computational approaches such as global energy optimization, simulated annealing, and structural bioinformatics. The optimal atomic-resolution structures of prion AGAAAAGA amyloid fibils reported in this paper have a value to the scientific community in its drive to find treatments for prion diseases.

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Section: Introductionmentioning

confidence: 99%

Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils

Zhang

Sun

2011

Journal of Theoretical Biology

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Optimal molecular structures of prion AGAAAAGA amyloid fibrils formatted by simulated annealing

Zhang

2010

J Mol Model

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To date, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins, although many experimental studies have shown that this region has amyloid fibril forming properties. This region belongs to the N-terminal unstructured region (1-123) of prions, the structure of which has proved hard to determine using NMR or X-ray crystallography. This paper reports the successful construction of three amyloid fibril models for this region. The models were formatted by standard simulated annealing using suitable templates from the Protein Data Bank, and were refined using several traditional optimization methods within AMBER. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, these models can be used as a reference for experimental studies on this region. The results presented here confirm standard simulated annealing as an effective tool in molecular modeling. The three constructed models for amyloid fibrils may be useful in furthering the goals of medicinal chemistry in this field.

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Some improved Dai–Yuan conjugate gradient methods for large-scale unconstrained optimization problems

Bojari,

Eslahchi

2023

J. Appl. Math. Comput.

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Global Convergence of a Special Case of the Dai–yuan Family Without Line Search

Cited by 3 publications

References 16 publications

Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils

Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils

Optimal molecular structures of prion AGAAAAGA amyloid fibrils formatted by simulated annealing

Some improved Dai–Yuan conjugate gradient methods for large-scale unconstrained optimization problems

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