ArticleJournal of chemical information and modeling2022
Developing Bonded Potentials for a Coarse-Grained Model of Intrinsically Disordered Proteins.
Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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Who cites it
19 citing papers in PubMed, 31 citations in OpenAlex.
- Accurate interdomain contacts in a mixed folded protein from NMR-guided coarse-grained simulations.Physical chemistry chemical physics : PCCP · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Multiscale Simulations Elucidate the Mechanism of Polyglutamine Aggregation and the Role of Flanking Domains in Fibril Polymorphism.The journal of physical chemistry. B · 2025Article
- Repulsive vs Attractive Crowding Distinctly Regulate TDP-43 Condensates through Region-specific Structural Dynamics.JACS Au · 2025Article
- Current practices in the study of biomolecular condensates: a community comment.Nature communications · 2025Article
- Transient Interdomain Interactions Modulate the Monomeric Structural Ensemble and Self-Assembly of Huntingtin Exon 1.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Multiscale simulations elucidate the mechanism of polyglutamine aggregation and the role of flanking domains in fibril polymorphism.bioRxiv : the preprint server for biology · 2025Article
- Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates.Nature communications · 2025Article
- Nanopores with an Engineered Selective Entropic Gate Detect Proteins at Nanomolar Concentration in Complex Biological Sample.Journal of the American Chemical Society · 2025Article
- COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins.Journal of chemical theory and computation · 2025Article
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins.Bioinformatics (Oxford, England) · 2024Article
- Backbone interactions and secondary structures in phase separation of disordered proteins.Biochemical Society transactions · 2024Review
- Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation.Journal of the American Chemical Society · 2024Article
- Complex Conformational Space of the RNA Polymerase II C-Terminal Domain upon Phosphorylation.The journal of physical chemistry. B · 2023Article
- Challenges in studying the liquid-to-solid phase transitions of proteins using computer simulations.Current opinion in chemical biology · 2023Review
- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Modeling Concentration-dependent Phase Separation Processes Involving Peptides and RNA via Residue-Based Coarse-Graining.Journal of chemical theory and computation · 2023Article
- RNA-Protein Assemblies: A Review of Biophysical Principles and Coarse-Grained Modeling Approaches.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Recent advances in residue-level coarse-grained (CG) computational models have enabled molecular-level insights into biological condensates of intrinsically disordered proteins (IDPs), shedding light on the sequence determinants of their phase separation. The existing CG models that treat protein chains as flexible molecules connected via harmonic bonds cannot populate common secondary-structure elements. Here, we present a CG dihedral angle potential between four neighboring beads centered at C
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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.