ArticleJournal of chemical information and modeling2015
Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins.
Article in Journal of chemical information and modeling, 2015. 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.
- Targeting protein disorder: the next hurdle in drug discovery.Nature reviews. Drug discovery · 2025Review
- Small-Molecule Inhibitors of Amyloid Beta: Insights from Molecular Dynamics-Part B: Natural Compounds.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Amber ff24EXP-GA, Based on Empirical Ramachandran Distributions of Glycine and Alanine Residues in Water.Journal of chemical theory and computation · 2025Article
- Small-Molecule Inhibitors of Amyloid Beta: Insights from Molecular Dynamics-Part A: Endogenous Compounds and Repurposed Drugs.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide.Proteins · 2023Article
- Balanced Force Field ff03CMAP Improving the Dynamics Conformation Sampling of Phosphorylation Site.International journal of molecular sciences · 2022Article
- NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins.Chemical reviews · 2022Review
- Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry.Chemical reviews · 2022Review
- An Overview of Several Inhibitors for Alzheimer's Disease: Characterization and Failure.International journal of molecular sciences · 2021Review
- Recent Force Field Strategies for Intrinsically Disordered Proteins.Journal of chemical information and modeling · 2021Review
- Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure.Journal of molecular biology · 2021Article
- Development of Charge-Augmented Three-Point Water Model (CAIPi3P) for Accurate Simulations of Intrinsically Disordered Proteins.International journal of molecular sciences · 2020Article
- Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins.Journal of chemical information and modeling · 2020Article
- Enhanced Molecular Dynamics Simulations of Intrinsically Disordered Proteins.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Well-Balanced Force FieldJournal of chemical theory and computation · 2019Article
- Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins.Physical chemistry chemical physics : PCCP · 2019Article
- Article
- Computational Studies of Intrinsically Disordered Proteins.The journal of physical chemistry. B · 2018Article
- Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB.The Journal of chemical physics · 2018Article
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5 authors.
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Abstract
Over 40% of eukaryotic proteomic sequences have been predicted to be intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) and confirmed to be associated with many diseases. However, widely used force fields cannot well reproduce the conformers of IDPs. Previously the ff99IDPs force field was released to simulate IDPs with CMAP energy corrections for the eight disorder-promoting residues. In order to further confirm the performance of ff99IDPs, three representative IDP systems (arginine-rich HIV-1 Rev, aspartic proteinase inhibitor IA3, and α-synuclein) were used to test and evaluate the simulation results. The results show that for free disordered proteins, the chemical shifts from the ff99IDPs simulations are in quantitative agreement with those from reported NMR measurements and better than those from ff99SBildn. Thus, ff99IDPs can sample more clusters of disordered conformers than ff99SBildn. For structural proteins, both ff99IDPs and ff99SBildn can well reproduce the conformations. In general, ff99IDPs can successfully be used to simulate the conformations of IDPs and IDRs in both bound and free states. However, relative errors could still be found at the boundaries of ordered residues scattered in long disorder-promoting sequences. Therefore, polarizable force fields might be one of the possible ways to further improve the performance on IDPs.
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