Amino-acid-dependent main-chain torsion-energy terms for protein systems

作者：Sakae Yoshitake^*; Okamoto Yuko

来源：Journal of Chemical Physics, 2013, 138(6): 064103.

DOI：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 psi (N-C-alpha-C-N) and zeta (C-beta-C-alpha-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 alpha-helical and beta-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.

• 出版日期2013-2-14