Name
Title | ||
|---|---|---|
Hamiltonian Reweighing to refine Protein Backbone Dihedral-Angle Parameters in the GROMOS Force Field. |
Abstract | ||
|---|---|---|
Molecular dynamics simulations of proteins depend critically on the underlying force field, which may be parameterized against experimental data or high-quality quantum calculations. Here, we develop search algorithms based on Monte Carlo and steepest descent calculations to optimize the backbone dihedral angle parameters from a single reference simulation. We apply these tools to improve the agreement between simulations of single, capped amino acids and experimentally determined J values and secondary structure propensities of these molecules. The parameters are further refined based on simulations of a set of seven proteins and finally validated in simulations on a large set of 52 protein structures. Improvements in the dihedral angle distributions are observed, and structural propensities of the proteins are reproduced very well. Overall, the GROMOS 54A8_bb parameter set forms an improvement to previous parameter sets, both for small molecules and for protein simulations. |
Year | DOI | Venue |
|---|---|---|
2020 | 10.1021/acs.jcim.9b01034 | JOURNAL OF CHEMICAL INFORMATION AND MODELING |
DocType | Volume | Issue |
Journal | 60 | 1 |
ISSN | Citations | PageRank |
1549-9596 | 0 | 0.34 |
References | Authors | |
0 | 2 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Matthias Diem | 1 | 0 | 0.34 |
| Chris Oostenbrink | 2 | 297 | 38.41 |