ReviewChemical Society reviews2014
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.
Review in Chemical Society reviews, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
What it found
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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
48 citing papers in PubMed.
- Valency-Limited Molecular Dynamics Simulations of Stickers-and-Spacers Polymers Reveal a Tradeoff Between Condensation and Organization.bioRxiv : the preprint server for biology · 2026Article
- MOFF2: A Transferable Coarse-Grained Protein Force Field for Predictive Condensate Simulations.bioRxiv : the preprint server for biology · 2026Article
- Aggregation of Intrinsically Fluorescent Proteins: Combining Coarse-Grained Molecular Dynamics with Alphafold Predictions.ACS omega · 2025Article
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Evaluation of Essential Dynamics and Fixed-Length Coarse Graining for Multidomain Proteins.The journal of physical chemistry. B · 2024Article
- GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems.Nature communications · 2024Article
- Mapping the configurational landscape and aggregation phase behavior of the tau protein fragment PHF6.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Top-Down Machine Learning of Coarse-Grained Protein Force Fields.Journal of chemical theory and computation · 2023Article
- Hydrophobic Homopolymer's Coil-Globule Transition and Adsorption onto a Hydrophobic Surface under Different Conditions.The journal of physical chemistry. B · 2023Article
- Optimized OPEP Force Field for Simulation of Crowded Protein Solutions.The journal of physical chemistry. B · 2023Article
- Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death.ACS central science · 2023Article
- A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution.Frontiers in bioinformatics · 2023Article
- Applications of Molecular Dynamics Simulation in Protein Study.Membranes · 2022Review
- Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.PLoS computational biology · 2022Article
- Effect of Cholesterol Molecules on Aβ1-42 Wild-Type and Mutants Trimers.Molecules (Basel, Switzerland) · 2022Article
- Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Exposure of Von Willebrand Factor Cleavage Site in A1A2A3-Fragment under Extreme Hydrodynamic Shear.Polymers · 2021Article
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.Chemical reviews · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
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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.