ReviewJournal of chemical information and modeling2021
Recent Force Field Strategies for Intrinsically Disordered Proteins.
Review in Journal of chemical information and modeling, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
46 citing papers in PubMed, 124 citations in OpenAlex.
- Article
- Article
- Nearest-Neighbor Effects in Short Unfolded Peptides: An Assessment of Molecular Dynamics Force Fields.Journal of chemical information and modeling · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Epigallocatechin Gallate as a State-Dependent Modulator of Amyloid-Biomolecules · 2026Review
- Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework.PLoS computational biology · 2026Article
- Computational perspectives on tubulin E-hook structure and mechanisms.Biophysical reports · 2026Review
- Using Multiple Isotope-Labeled Infrared Spectra for the Structural Characterization of an Intrinsically Disordered Peptide.The journal of physical chemistry. B · 2025Article
- An Adaptive Force Matching Potential for Alanine Developed with Møller-Plesset Perturbation Theory and Smooth Fourier Transform Correction Map.The journal of physical chemistry. B · 2025Article
- Biomolecular Condensates as Emerging Biomaterials: Functional Mechanisms and Advances in Computational and Experimental Approaches.Advanced materials (Deerfield Beach, Fla.) · 2025Review
- In Silico discovery of novel androgen receptor inhibitors for prostate cancer therapy using virtual screening, molecular docking, and molecular dynamics simulations.Scientific reports · 2025Article
- Nanopores with an Engineered Selective Entropic Gate Detect Proteins at Nanomolar Concentration in Complex Biological Sample.Journal of the American Chemical Society · 2025Article
- Martini3-IDP: improved Martini 3 force field for disordered proteins.Nature communications · 2025Article
- Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning.Journal of chemical information and modeling · 2025Article
- Use of AI-methods over MD simulations in the sampling of conformational ensembles in IDPs.Frontiers in molecular biosciences · 2025Review
- Liquid-Liquid Phase Separation Associated with Intrinsically Disordered Proteins: Experimental and Computational Tools.Current protein & peptide science · 2025Review
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Clustering of RNA Polymerase II C-Terminal Domain Models upon Phosphorylation.The journal of physical chemistry. B · 2024Article
- Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering.Journal of chemical information and modeling · 2024Article
- Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study.Journal of chemical information and modeling · 2024Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Intrinsically disordered proteins (IDPs) are widely distributed across eukaryotic cells, playing important roles in molecular recognition, molecular assembly, post-translational modification, and other biological processes. IDPs are also associated with many diseases such as cancers, cardiovascular diseases, and neurodegenerative diseases. Due to their structural flexibility, conventional experimental methods cannot reliably capture their heterogeneous structures. Molecular dynamics simulation becomes an important complementary tool to quantify IDP structures. This review covers recent force field strategies proposed for more accurate molecular dynamics simulations of IDPs. The strategies include adjusting dihedral parameters, adding grid-based energy correction map (CMAP) parameters, refining protein-water interactions, and others. Different force fields were found to perform well on specific observables of specific IDPs but also are limited in reproducing all available experimental observables consistently for all tested IDPs. We conclude the review with perspective areas for improvements for future force fields for IDPs.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.