ReviewCurrent opinion in structural biology2022
Unifying coarse-grained force fields for folded and disordered proteins.
Review in Current opinion in structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed, 50 citations in OpenAlex.
- The filamentous ultrastructure of the PopZ condensate is required for its cellular function.Nature structural & molecular biology · 2026Article
- Nucleosome condensate and linker DNA alter chromatin folding pathways and rates.Biophysical journal · 2026Article
- Heterogeneous condensates of transcription factors in embryonic stem cells: Molecular simulations.Biophysical journal · 2025Article
- The ribonucleoprotein hnRNPA1 mediates binding to RNA and DNA telomeric G-quadruplexes through an RGG-rich region.The Journal of biological chemistry · 2025Article
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Microphase separation produces interfacial environment within diblock biomolecular condensates.eLife · 2025Article
- Integrative spatiotemporal modeling of biomolecular processes: Application to the assembly of the nuclear pore complex.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Integrative spatiotemporal modeling of biomolecular processes: application to the assembly of the Nuclear Pore Complex.bioRxiv : the preprint server for biology · 2024Article
- Microphase Separation Produces Interfacial Environment within Diblock Biomolecular Condensates.bioRxiv : the preprint server for biology · 2024Article
- A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta.International journal of molecular sciences · 2024Article
- Micropolarity governs the structural organization of biomolecular condensates.Nature chemical biology · 2024Article
- Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks.ACS central science · 2023Article
- Transferable Coarse Graining via Contrastive Learning of Graph Neural Networks.bioRxiv : the preprint server for biology · 2023Article
- OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates.PLoS computational biology · 2023Article
- Challenges in studying the liquid-to-solid phase transitions of proteins using computer simulations.Current opinion in chemical biology · 2023Review
- Toward a general neural network force field for protein simulations: Refining the intramolecular interaction in protein.The Journal of chemical physics · 2023Article
- OpenABC Enables Flexible, Simplified, and Efficient GPU Accelerated Simulations of Biomolecular Condensates.bioRxiv : the preprint server for biology · 2023Article
- Chemical tools for study and modulation of biomolecular phase transitions.Chemical science · 2022Review
- Molecular Determinants for the Layering and Coarsening of Biological Condensates.Aggregate (Hoboken, N.J.) · 2022Article
- Principles Governing the Phase Separation of Multidomain Proteins.Biochemistry · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Liquid-liquid phase separation drives the formation of biological condensates that play essential roles in transcriptional regulation and signal sensing. Computational modeling could provide high-resolution structural characterizations of these condensates and help uncover physicochemical interactions that dictate their stability. However, many protein molecules involved in phase separation often contain multiple ordered domains connected with flexible, structureless linkers. Simulating such proteins necessitates force fields with consistent accuracy for both folded and disordered proteins. We provide a critical review of existing coarse-grained force fields for disordered proteins and highlight the challenges in their application to folded proteins. After discussing existing algorithms for force field parameterization, we propose an optimization strategy that should lead to computer models with improved transferability across protein types.
Indexed as
Identifiers
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.