ArticleJournal of chemical theory and computation2019
Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- HyRes: Accurate Physics-Based Simulation of Dynamic Protein Structures and Interactions in Complex Environments at Scale.bioRxiv : the preprint server for biology · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Atomic resolution ensembles of intrinsically disordered proteins with Alphafold.Nature communications · 2026Article
- Coil-Library-Derived Amino-Acid-Specific Side-Chain χJournal of chemical theory and computation · 2025Article
- Use of AI-methods over MD simulations in the sampling of conformational ensembles in IDPs.Frontiers in molecular biosciences · 2025Review
- Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations.JACS Au · 2024Article
- Phosphorylation of disordered proteins tunes local and global intramolecular interactions.Biophysical journal · 2024Article
- Phosphorylation of disordered proteins tunes local and global intramolecular interactions.bioRxiv : the preprint server for biology · 2024Article
- Thermodynamic modulation of gephyrin condensation by inhibitory synapse components.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions.Journal of chemical information and modeling · 2022Article
- Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry.Chemical reviews · 2022Review
- Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains.Nature chemistry · 2022Article
- Unifying coarse-grained force fields for folded and disordered proteins.Current opinion in structural biology · 2022Review
- When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes.Biomolecules · 2021Review
- Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.Biomolecules · 2021Review
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- Learning the protein language: Evolution, structure, and function.Cell systems · 2021Article
- Physics-based computational and theoretical approaches to intrinsically disordered proteins.Current opinion in structural biology · 2021Review
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2 authors.
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Abstract
We present an improved version of the ABSINTH implicit solvation model and force field paradigm (termed ABSINTH-C) by incorporating a grid-based term that bootstraps against experimentally derived and computationally optimized conformational statistics for blocked amino acids. These statistics provide high-resolution descriptions of the intrinsic backbone dihedral angle preferences for all 20 amino acids. The original ABSINTH model generates Ramachandran plots that are too shallow in terms of the basin structures and too permissive in terms of dihedral angle preferences. We bootstrap against the reference optimized landscapes and incorporate CMAP-like residue-specific terms that help us reproduce the intrinsic dihedral angle preferences of individual amino acids. These corrections that lead to ABSINTH-C are achieved by balancing the incorporation of the new residue-specific terms with the accuracies inherent to the original ABSINTH model. We demonstrate the robustness of ABSINTH-C through a series of examples to highlight the preservation of accuracies as well as examples that demonstrate the improvements. Our efforts show how the recent experimentally derived and computationally optimized coil-library landscapes can be used as a touchstone for quantifying errors and making improvements to molecular mechanics force fields.
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