ArticlePhysical chemistry chemical physics : PCCP2019
Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins.
Article in Physical chemistry chemical physics : PCCP, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Multiscale Neural Network Potential with Anisotropic Message Passing for the Fast and Accurate Simulation of Protein Dynamics and Enzymatic Reactions.Journal of the American Chemical Society · 2026Article
- How Well Do Molecular Dynamics Force Fields Model Peptides: A Systematic Benchmark across Diverse Folding Behaviors.The journal of physical chemistry. B · 2026Article
- Small-Molecule Inhibitors of Amyloid Beta: Insights from Molecular Dynamics-Part B: Natural Compounds.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Small-Molecule Inhibitors of Amyloid Beta: Insights from Molecular Dynamics-Part A: Endogenous Compounds and Repurposed Drugs.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes.ArXiv · 2024Article
- Toward a general neural network force field for protein simulations: Refining the intramolecular interaction in protein.The Journal of chemical physics · 2023Article
- Review
- Discovery of a Novel Inhibitor Structure ofMolecules (Basel, Switzerland) · 2022Article
- Self-Diffusive Properties of the Intrinsically Disordered Protein Histatin 5 and the Impact of Crowding Thereon: A Combined Neutron Spectroscopy and Molecular Dynamics Simulation Study.The journal of physical chemistry. B · 2022Article
- Computational Models for the Study of Protein Aggregation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity.Journal of chemical theory and computation · 2021Article
- An Overview of Several Inhibitors for Alzheimer's Disease: Characterization and Failure.International journal of molecular sciences · 2021Review
- Fisetin inhibits tau aggregation by interacting with the protein and preventing the formation of β-strands.International journal of biological macromolecules · 2021Article
- Folding and self-assembly of short intrinsically disordered peptides and protein regions.Nanoscale advances · 2021Review
- Exploring the conformational dynamics and flexibility of intrinsically disordered HIV-1 Nef protein using molecular dynamic network approaches.3 Biotech · 2021Article
- Recent Force Field Strategies for Intrinsically Disordered Proteins.Journal of chemical information and modeling · 2021Review
- High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme.Nature communications · 2021Article
- The F19W mutation reduces the binding affinity of the transmembrane AβRSC advances · 2021Article
- Identification of an α-MoRF in the Intrinsically Disordered Region of the Escargot Transcription Factor.ACS omega · 2020Article
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6 authors.
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Abstract
Intrinsically disordered proteins (IDPs) have received increasing attention in recent studies due to their structural heterogeneity and critical biological functions. To fully understand the structural properties and determine accurate ensembles of IDPs, molecular dynamics (MD) simulation was widely used to sample diverse conformations and reveal the structural dynamics. However, the classical state-of-the-art force fields perform well for folded proteins while being unsatisfactory for the simulations of disordered proteins reported in many previous studies. Thus, improved force fields were developed to precisely describe both folded proteins and disordered proteins. Preliminary tests show that our newly developed CHARMM36IDPSFF (C36IDPSFF) force field can well reproduce the experimental observables of several disordered proteins, but more tests on different types of proteins are needed to further evaluate the performance of C36IDPSFF. Here, we extensively simulate short peptides, disordered proteins, and fast-folding proteins as well as folded proteins, and compare the simulated results with the experimental observables. The simulation results show that C36IDPSFF could substantially reproduce the experimental observables for most of the tested proteins but some limitations are also found in the radius of gyration of large disordered proteins and the stability of fast-folding proteins. This force field will facilitate large scale studies of protein structural dynamics and functions using MD simulations.
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