NepoIP/MM: Towards Accurate Biomolecular Simulation with a Machine Learning/Molecular Mechanics Model Incorporating Polarization Effects
Published in preprint, 2025
Recommended citation: arXiv:2502.02801 https://arxiv.org/abs/2502.02801
Selected Publications
For full list of publication: Google Scholar profile. or: Researchgate profile.
Excited-Ground State Transition of RNA Strand Slippage Mechanism Captured by Base-specific Force Field
Published in Journal of Chemical Theory and Computation, 2024
Our results of capturing the strand slippage, excited-ground transition, de novo folding, and simulations for various typical RNA motifs indicate that BSFF2 should be one of valuable tools for dynamic conformation research and structure prediction of RNA, and a future contribution to RNA-targeted drug design as well as RNA therapy development.
Recommended citation: J. Chem. Theory Comput. 2024, 20, 14, 6082–6097 https://pubs.acs.org/doi/10.1021/acs.jctc.4c00497
Phosphorylation Modification Force Field FB18CMAP Improving Conformation Sampling of Phosphoproteins
Published in Journal of Chemical Information and Modeling, 2023
Here, a new force field parameter (named FB18CMAP) is generated by fitting against quantum mechanics (QM) energy in aqueous solution with phi/psi dihedral potential-energy surfaces optimized using CMAP parameters.
Recommended citation: Song, G., et al., Phosphorylation Modification Force Field FB18CMAP Improving Conformation Sampling of Phosphoproteins. Journal of Chemical Information and Modeling 2023, 63, 1602-1614. https://pubs.acs.org/doi/10.1021/acs.jcim.3c00112