ArticleThe journal of physical chemistry letters2016
Performance of Protein-Ligand Force Fields for the Flavodoxin-Flavin Mononucleotide System.
Article in The journal of physical chemistry letters, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Venetoclax Decreases the Expression of the Spike Protein through Amino Acids Q493 and S494 in SARS-CoV-2.Cells · 2022Article
- Computational Models for the Study of Protein Aggregation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Development and Testing of the OPLS-AA/M Force Field for RNA.Journal of chemical theory and computation · 2019Article
- Improved Treatment of Nucleosides and Nucleotides in the OPLS-AA Force Field.Chemical physics letters · 2017Article
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3 authors.
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Abstract
The ability to accurately perform molecular dynamics and free energy perturbation calculations for protein-ligand systems is of broad interest to the biophysical and pharmaceutical sciences. In this work, several popular force fields are evaluated for reproducing experimental properties of the flavodoxin/flavin mononucleotide system. Calculated (3)J couplings from molecular dynamics simulations probing φ and χ1 dihedral angles are compared to over 1000 experimental measurements. Free energy perturbation calculations were also executed between different protein mutants for comparison with experimental data for relative free energies of binding. Newer versions of popular protein force fields reproduced (3)J backbone and side chain couplings with good accuracy, with RMSD values near or below one hertz in most cases. OPLS-AA/M paired with CM5 charges for the ligand performed particularly well, both for the (3)J couplings and FEP results, with a mean unsigned error for relative free energies of binding of 0.36 kcal/mol.
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