ArticleJournal of chemical theory and computation2025
Amber ff24EXP-GA, Based on Empirical Ramachandran Distributions of Glycine and Alanine Residues in Water.
Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Nearest-Neighbor Effects in Short Unfolded Peptides: An Assessment of Molecular Dynamics Force Fields.Journal of chemical information and modeling · 2026Article
- Nearest neighbour interactions between amino acid residues in short peptides and coil libraries.RSC advances · 2026Article
- Sequence-Dependent Heterotypic Assemblies of Intrinsically Disordered Peptides.ChemistryEurope · 2026Article
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3 authors.
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Abstract
Molecular dynamics (MD) offers important insights into intrinsically disordered peptides and proteins (IDPs) at a level of detail that often surpasses that available through experiments. Recent studies indicate that MD force fields do not reproduce intrinsic conformational ensembles of amino acid residues in water well, which limits their applicability to IDPs. We report a new MD force field, Amber ff24EXP-GA, derived from Amber ff14SB by optimizing the backbone dihedral potentials for guest glycine and alanine residues in cationic GGG and GAG peptides, respectively, to best match the guest residue-specific spectroscopic data. Amber ff24EXP-GA outperforms Amber ff14SB with respect to conformational ensembles of all 14 guest residues x (G, A, L, V, I, F, Y, D
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