ArticleJournal of chemical theory and computation2025
COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins.
Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- 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
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Enhanced Condensation of RNA Repeats Induced by Terahertz Oscillatory Fields.Molecules (Basel, Switzerland) · 2026Article
- Transient tertiary structure in intrinsically disordered proteins revealed by multithermal enhanced sampling.Nature communications · 2026Article
- Toward a unified framework for determining conformational ensembles of disordered proteins.Nature methods · 2026Review
- 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
- Deep generative modeling of temperature-dependent structural ensembles of proteins.Communications chemistry · 2025Article
- How the Extent of Protein Folding and Oligomerization Modulate Condensate Formation and Properties.The journal of physical chemistry letters · 2025Article
- Repulsive vs Attractive Crowding Distinctly Regulate TDP-43 Condensates through Region-specific Structural Dynamics.JACS Au · 2025Article
- A Hybrid UA-CG Force Field for Aggregation Simulation of Amyloidogenic Peptide via Liquid-like Intermediates.Molecules (Basel, Switzerland) · 2025Article
- A coarse-grained model for disordered proteins under crowded conditions.Protein science : a publication of the Protein Society · 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
- Modeling biomolecular condensates across scales: Atomistic, coarse-grained, and data-driven approaches.Advances in physics: X · 2025Article
- RNA-Protein Assemblies: A Review of Biophysical Principles and Coarse-Grained Modeling Approaches.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
- Erratum issued
- Update of
Authors and funding
4 authors.
Funding
Abstract
Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.
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