2013/01/07 by Yoshitake Sakae, Sakae, Yoshitake, Yuko Okamoto +1
Biochemistry, Genetics and Molecular Biology · Materials Science · Physics and Astronomy · #Biological Physics (physics.bio-ph) #Chemical Physics (physics.chem-ph) #Computational Physics (physics.comp-ph) #Enzyme Structure and Function #FOS: Physical sciences #Protein Structure and Dynamics #RNA and protein synthesis mechanisms #Statistical Mechanics (cond-mat.stat-mech) #cond-mat.stat-mech #physics.bio-ph #physics.chem-ph #physics.comp-ph
paper · pdf · doi:10.48550/arxiv.1301.1169
10 pages, (Revtex4.1), 6 figures. arXiv admin note: substantial text overlap with arXiv:1208.6150, arXiv:1206.3909
arxiv created 2013/01/07 · openalex publication_date 2013/01/07 · arxiv updated 2013/01/08 · openalex created_date 2016/08/23 · openalex updated_date 2026/07/28
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those obtained by molecular dynamics simulations is used as a criterion for the optimization of force-field parameters. As an example of the applications of the present method, we refined the force-field parameter set of the AMBER ff99SB force field by searching the torsion-energy parameter spaces of ψ (N-Cα-C-N) and ζ (Cβ-Cα-C-N) of the backbone dihedral angles. 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 ff99SB force field.