ArticleJournal of chemical information and modeling2020
Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins.
Article in Journal of chemical information and modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Accurate Generation of Conformational Ensembles for Intrinsically Disordered Proteins with IDPFold.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A Computational Approach to Characterize the Protein S-Mer Tyrosine Kinase (PROS1-MERTK) Protein-Protein Interaction Dynamics.Cell biochemistry and biophysics · 2025Article
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 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
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Amino Acid Residue-Specific Ramachandran Distributions Derived from a Simple Mean Field Potential.ACS physical chemistry Au · 2024Article
- Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations.Journal of chemical information and modeling · 2024Article
- Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities.Biophysical journal · 2024Article
- Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling.Briefings in bioinformatics · 2023Article
- Intrinsic disorder may drive the interaction of PROS1 and MERTK in uveal melanoma.International journal of biological macromolecules · 2023Article
- Toward a general neural network force field for protein simulations: Refining the intramolecular interaction in protein.The Journal of chemical physics · 2023Article
- Enhancing Conformational Sampling for Intrinsically Disordered and Ordered Proteins by Variational Autoencoder.International journal of molecular sciences · 2023Article
- Review
- Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide.Proteins · 2023Article
- Activation of p53: How phosphorylated Ser15 triggers sequential phosphorylation of p53 at Thr18 by CK1δ.Proteins · 2022Article
- Incorporation of DThe journal of physical chemistry. B · 2022Article
- Balanced Force Field ff03CMAP Improving the Dynamics Conformation Sampling of Phosphorylation Site.International journal of molecular sciences · 2022Article
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Authors and funding
4 authors.
Funding
Abstract
The need for accurate and efficient force fields for modeling 3D structures of macrobiomolecules and in particular intrinsically disordered proteins (IDPs) has increased with recent findings to associate IDPs and human diseases. However, most conventional protein force fields and recent IDP-specific force fields are limited in reproducing accurate structural features of IDPs. Here, we present an environmental specific precise force field (ESFF1) based on CMAP corrections of 71 different sequence environments to improve the accuracy and efficiency of MD simulation for both IDPs and folded proteins. MD simulations of 84 different short peptides, IDPs, and structured proteins show that
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