ff19SB: Amino-acid specific protein backbone parameters trained against quantum mechanics energy surfaces in solution
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Summary
The results show that ff19SB, when combined with a more accurate water model such as OPC, should have better predictive power for modeling sequence-specific behavior, protein mutations, and also rational protein design.
- Type
- article
- Published
- 2019-06-17
- Cited by
- 2,182
- References
- 122
- Access
- Open access
- OpenAlex
- https://openalex.org/W2989052455
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:207936044
Keywords
Ramachandran plot, Dihedral angle, Molecular dynamics, Force field (fiction), Molecular mechanics
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- Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4
- Hamiltonian Reweighing to refine Protein Backbone Dihedral-Angle Parameters in the GROMOS Force Field.
- Protein Dynamics and the Folding Degree
- Computational Prediction of Mutational Effects on SARS-CoV-2 Binding by Relative Free Energy Calculations
- Water-Mediated Electronic Structure of Oligopeptides Probed by Their UV Circular Dichroism, Absorption Spectra, and Time-Dependent DFT Calculations.
- Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering
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- Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies
- Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models
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- Hybrid Alchemical Free Energy/Machine-Learning Methodology for the Computation of Hydration Free Energies
- On the Case of the Misplaced Hydrogens
- Glycine in Water Favors the Polyproline II State
- Flavonoids and Terpenoids with PTP-1B Inhibitory Properties from the Infusion of Salvia amarissima Ortega
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