ArticleThe journal of physical chemistry letters2015
Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins.
Article in The journal of physical chemistry letters, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Amino Acid Residue-Specific Ramachandran Distributions Derived from a Simple Mean Field Potential.ACS physical chemistry Au · 2024Article
- A backbone-dependent rotamer library with high (ϕ, ψ) coverage using metadynamics simulations.Protein science : a publication of the Protein Society · 2022Article
- The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer.Autophagy · 2021Article
- Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties.The journal of physical chemistry letters · 2019Article
- Protein dynamics and structural waters in bromodomains.PloS one · 2017Article
- Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization.The journal of physical chemistry. B · 2016Article
- Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation.The Journal of chemical physics · 2015Article
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2 authors.
Funding
Abstract
A recent report of (3)J(HNHα) scalar coupling constants for hundreds of two-residue peptides has provided an important opportunity to test simulation force fields for proteins. Here, we compare the abilities of three derivatives of the Amber ff99SB force field to reproduce these data. We report molecular dynamics (MD) simulations of 256 two-residue peptides and show that the recently developed residue-specific force field (RSFF2) produces a dramatic improvement in the agreement with experimental (3)J(HNHα) coupling constants. We further show that RSFF2 also appears to produce a modest improvement in reproducing the (3)J(HNHα) coupling constants of five model proteins. Perhaps surprisingly, an analysis of neighboring residue effects (NREs) on the (3)J(HNHα) coupling constants of the two-residue peptides indicates little difference between the force fields' abilities to reproduce experimental NREs. We speculate that this might indicate limitations in the force fields' descriptions of nonbonded interactions between adjacent side chains or with terminal capping groups.
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