ArticleJournal of chemical information and modeling2017
The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins.
Article in Journal of chemical information and modeling, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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Who cites it
81 citing papers in PubMed.
- Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- How Well Do Molecular Dynamics Force Fields Model Peptides: A Systematic Benchmark across Diverse Folding Behaviors.The journal of physical chemistry. B · 2026Article
- Mechanistic insights into PCBP1-driven unfolding of selected i-motif DNA at GNature communications · 2026Article
- Integrating AI-Based Clustering, Molecular Dynamics, and Binding Energy Analysis to Elucidate Conformational Dynamics and Binding Selectivity in Extracellular Signal-Regulated Kinases 1 and 2 Complexes.Bioinformatics and biology insights · 2026Article
- Oleuropein Aglycone, an Olive Polyphenol, Influences Alpha-Synuclein Aggregation and Exerts Neuroprotective Effects in Different Parkinson's Disease Models.Molecular neurobiology · 2025Article
- Small-Molecule Inhibitors of Amyloid Beta: Insights from Molecular Dynamics-Part B: Natural Compounds.Pharmaceuticals (Basel, Switzerland) · 2025Review
- A Computational Approach to Characterize the Protein S-Mer Tyrosine Kinase (PROS1-MERTK) Protein-Protein Interaction Dynamics.Cell biochemistry and biophysics · 2025Article
- Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning.Journal of chemical information and modeling · 2025Article
- Controlled by disorder: Phosphorylation modulates SRSF1 domain availability for spliceosome assembly.Protein science : a publication of the Protein Society · 2025Article
- Small-Molecule Inhibitors of Amyloid Beta: Insights from Molecular Dynamics-Part A: Endogenous Compounds and Repurposed Drugs.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Use of AI-methods over MD simulations in the sampling of conformational ensembles in IDPs.Frontiers in molecular biosciences · 2025Review
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Intrinsic Disorder and Other Malleable Arsenals of Evolved Protein Multifunctionality.Journal of molecular evolution · 2024Review
- Comparison of Methodologies for Absolute Binding Free Energy Calculations of Ligands to Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2024Article
- What tunes guanine ionization potential in a nucleosome? An all-in-one systematic QM/MM assessment.Biophysical journal · 2024Article
- Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities.Biophysical journal · 2024Article
- A druggable conformational switch in the c-MYC transactivation domain.Nature communications · 2024Article
- Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Synthesis and degradation of the cyclic dinucleotide messenger c-di-AMP in the hyperthermophilic archaeon Pyrococcus yayanosii.Protein science : a publication of the Protein Society · 2023Article
21 more citing papers are in PubMed but not listed here.
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Abstract
Intrinsically disordered proteins (IDPs) or intrinsically disordered regions do not have a fixed tertiary structure but play key roles in signal regulation, molecule recognition, and drug targeting. However, it is difficult to study the structure and function of IDPs by traditional experimental methods because of their diverse conformations. Limitations of current generic protein force fields and solvent models were reported in the previous simulations of IDPs. We have also explored overcoming these limitations by developing the ff99IDPs and ff14IDPs force fields to correct the dihedral distribution for eight disorder-promoting residues often observed in IDPs and found encouraging improvements. Here we extend our correction of backbone dihedral terms to all 20 naturally occurring amino acids in the IDP-specific force field ff14IDPSFF to further improve the quality of the modeling of IDPs. Extensive tests of seven IDPs and 14 unstructured short peptides show that the simulated Cα chemical shifts obtained with the ff14IDPSFF force field are in quantitative agreement with those from NMR experiments and are more accurate than those obtained with the base generic force field and also our previous ff14IDPs that only corrects the eight disorder-promoting amino acids. The influence of the solvent model was also investigated and found to be less important. Finally, our explicit-solvent MD simulations further show that ff14IDPSFF can still be used to model structural and dynamical properties of two tested folded proteins, with a slightly better agreement in the loop regions for both structural and dynamical properties. These findings confirm that the newly developed IDP-specific force field ff14IDPSFF can improve the conformer sampling of intrinsically disordered proteins.
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