{"paper":{"title":"Optimizations of force-field parameters for protein systems with the secondary-structure stability and instability","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cond-mat.stat-mech","physics.chem-ph","physics.comp-ph"],"primary_cat":"physics.bio-ph","authors_text":"Yoshitake Sakae, Yuko Okamoto (Nagoya University)","submitted_at":"2013-01-07T12:30:44Z","abstract_excerpt":"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 $\\psi$ (N-C$^{\\alpha}$-C-N) and $\\zeta$ (C$^{\\beta}$-C$^{\\alpha}$-C-N) "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1301.1169","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}