2024-03-29T13:57:46Z
https://nagoya.repo.nii.ac.jp/oai
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2023-01-16T04:07:19Z
320:321:322
A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction
Sasaki, Takeshi N.
Cetin, Hikmet
Sasai, Masaki
open access
This is the author's version of a work that was accepted for publication in Biochemical and Biophysical Research Communications. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms, may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Biochemical and Biophysical Research Communications. v.369, n.2, 2008, p.500–506, DOI: 10.1016/j.bbrc.2008.02.048
Protein structure prediction
Langevin dynamics
Fragment assembly
De novo prediction of protein structures, the prediction of structures from amino acid sequences which are not similar to those of hitherto resolved structures, has been one of the major challenges in molecular biophysics. In this paper, we develop a new method of de novo prediction, which combines the fragment assembly method and the simulation of physical folding process: structures which have consistently assembled fragments are dynamically searched by Langevin molecular dynamics of conformational change. The benchmarking test shows that the prediction is improved when the candidate structures are cross-checked by an empirically derived score function.
Elsevier
2008-05
eng
journal article
AM
http://hdl.handle.net/2237/20616
https://nagoya.repo.nii.ac.jp/records/18530
https://doi.org/10.1016/j.bbrc.2008.02.048
0006-291X
Biochemical and Biophysical Research Communications
369
2
500
506
https://nagoya.repo.nii.ac.jp/record/18530/files/SasakiCetinSasaiBBRC2008.pdf
application/pdf
541.8 kB
2018-02-21