ArticleJournal of chemical theory and computation2023
Modeling Concentration-dependent Phase Separation Processes Involving Peptides and RNA via Residue-Based Coarse-Graining.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Recent advances in coarse-grained simulations of nucleic acid condensation.The Biochemical journal · 2026Review
- Article
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Article
- CondenSimAdapter: A Versatile Builder for Multiscale Simulations of Protein Condensates with Broad Force-Field Compatibility and Robust Dense-Phase Relaxation.Journal of chemical information and modeling · 2026Article
- HyRes: Accurate Physics-Based Simulation of Dynamic Protein Structures and Interactions in Complex Environments at Scale.bioRxiv : the preprint server for biology · 2026Article
- RNA helicase DDX6 governs ASC speck formation in P-bodies and the transition to stress granules via phase separation during inflammasome activation.Cell discovery · 2026Article
- Enhanced Condensation of RNA Repeats Induced by Terahertz Oscillatory Fields.Molecules (Basel, Switzerland) · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Accurate conformational ensembles of intrinsically disordered proteins using reweighting based on NMR chemical shifts.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Atomic resolution ensembles of intrinsically disordered proteins with Alphafold.Nature communications · 2026Article
- Aggregation of Intrinsically Fluorescent Proteins: Combining Coarse-Grained Molecular Dynamics with Alphafold Predictions.ACS omega · 2025Article
- Driving forces of RNA condensation revealed through coarse-grained modeling with explicit MgProceedings of the National Academy of Sciences of the United States of America · 2025Article
- A Hybrid UA-CG Force Field for Aggregation Simulation of Amyloidogenic Peptide via Liquid-like Intermediates.Molecules (Basel, Switzerland) · 2025Article
- All-atom simulations of biomolecular condensates.Current opinion in structural biology · 2025Review
- Generation of protein dynamics by machine learning.Current opinion in structural biology · 2025Review
- Accurate Predictions of Molecular Properties of Proteins via Graph Neural Networks and Transfer Learning.Journal of chemical theory and computation · 2025Article
- Prediction of phase-separation propensities of disordered proteins from sequence.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins.Journal of chemical theory and computation · 2025Article
- Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells.Journal of chemical information and modeling · 2024Review
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Authors and funding
4 authors.
Funding
Abstract
Biomolecular condensation, especially liquid-liquid phase separation, is an important physical process with relevance for a number of different aspects of biological functions. Key questions of what drives such condensation, especially in terms of molecular composition, can be addressed via computer simulations, but the development of computationally efficient yet physically realistic models has been challenging. Here, the coarse-grained model COCOMO is introduced that balances the polymer behavior of peptides and RNA chains with their propensity to phase separate as a function of composition and concentration. COCOMO is a residue-based model that combines bonded terms with short- and long-range terms, including a Debye-Hückel solvation term. The model is highly predictive of experimental data on phase-separating model systems. It is also computationally efficient and can reach the spatial and temporal scales on which biomolecular condensation is observed with moderate computational resources.
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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.