ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution
Stony Brook University · Brookhaven National Laboratory
Abstract
Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation, however, is highly determined by the molecular mechanics (MM) force field (FF), a set of functions with adjustable parameters to compute the potential energies from atomic positions. However, the overall quality of the FF, such as our previously published ff99SB and ff14SB, can be limited by assumptions that were made years ago. In the updated model presented here (ff19SB), we have significantly improved the backbone profiles for all 20 amino acids. We fit coupled φ/ψ parameters using 2D φ/ψ conformational scans for multiple amino acids, using as reference…
Citation impact
- FWCI
- 34.43
- Percentile
- 100%
- References
- 131
Authors
11Topics & keywords
- Ramachandran plot
- Dihedral angle
- Molecular dynamics
- Force field (fiction)
- Molecular mechanics
- Biomolecule
- Conformational isomerism
- Chemistry
- Affordable and clean energy
Funding
- NSNational Science FoundationAwards: 0725070, 1665159, 1238993, ACI-1238993, OCI-0725070, DE-SC0012704
- UDU.S. Department of EnergyAwards: OCI-0725070, ACI-1238993, 0725070, SC0012704
- SBStony Brook University
- NINational Institutes of HealthAwards: DE-SC0012704, K12GM102778
- OOOffice of ScienceAwards: OCI-0725070, ACI-1238993, SC0012704, DE-SC0012704
- NINational Institute of General Medical SciencesAward: K12GM102778
- BEBasic Energy SciencesAwards: DE-SC0012704, SC0012704
- LCLaufer Center for Physical and Quantitative Biology, Stony Brook University
- BNBrookhaven National LaboratoryAward: SC0012704