2024-03-29T15:18:33Z
https://nagoya.repo.nii.ac.jp/oai
oai:nagoya.repo.nii.ac.jp:00026925
2023-01-16T04:17:35Z
336:695:696
Amino-acid-dependent main-chain torsion-energy terms for protein systems
Sakae, Yoshitake
Okamoto, Yuko
open access
Copyright 2013 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing.The following article appeared in (The Journal of Chemical Physics. v.138, n.6, 2013, p.064103) and may be found at (http://dx.doi.org/10.1063/1.4774159).
Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters for main-chain torsion-energy terms. Here, we propose a new type of amino-acid-dependent torsion-energy terms in the force fields. As an example, we applied this approach to AMBER ff03 force field and determined new amino-acid-dependent parameters for ψ (N-C^α-C-N) and ζ (C^β-C^α-C-N) angles for each amino acid by using our optimization method, which is one of the knowledge-based approach. In order to test the validity of the new force-field parameters, we then performed folding simulations of α-helical and β-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff03 force field.
AIP Publishing
2013-02-14
eng
journal article
VoR
http://hdl.handle.net/2237/00029128
https://nagoya.repo.nii.ac.jp/records/26925
https://doi.org/10.1063/1.4774159
0021-9606
The Journal of Chemical Physics
138
6
064103
https://nagoya.repo.nii.ac.jp/record/26925/files/1_4774159.pdf
application/pdf
1.6 MB
2018-12-21