ArticleThe Journal of chemical physics2009
Generic coarse-grained model for protein folding and aggregation.
Article in The Journal of chemical physics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 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
- Multiscale simulations of folded and intrinsically disordered region-containing protein condensates.Biophysical journal · 2026Article
- Neurodegeneration Through the Lens of Bioinformatics Approaches: Computational Mechanisms of Protein Misfolding.International journal of molecular sciences · 2025Review
- Computational rheometry of viscoelastic networks: From random graphs to biomolecular condensates.bioRxiv : the preprint server for biology · 2025Article
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Backbone-mediated weakening of pairwise interactions enables percolation in peptide-based mimics of protein condensates.Communications chemistry · 2025Article
- The TEMPO integrator: accelerating molecular simulations by temporally multiscale force prediction.Bioinformatics advances · 2025Article
- Coarse-Grained Simulation Study of the Association of Selected Dipeptides.The journal of physical chemistry. B · 2024Article
- Monomer unfolding of a bacterial ESCRT-III superfamily member is coupled to oligomer disassembly.Protein science : a publication of the Protein Society · 2024Article
- A coarse-grained model for disordered and multi-domain proteins.Protein science : a publication of the Protein Society · 2024Article
- Toward Accurate Simulation of Coupling between Protein Secondary Structure and Phase Separation.Journal of the American Chemical Society · 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
- Challenges in studying the liquid-to-solid phase transitions of proteins using computer simulations.Current opinion in chemical biology · 2023Review
- Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining.Journal of chemical information and modeling · 2023Article
- Machine learned coarse-grained protein force-fields: Are we there yet?Current opinion in structural biology · 2023Review
- Slicing and Dicing: Optimal Coarse-Grained Representation to Preserve Molecular Kinetics.ACS central science · 2023Article
- Toward Accurate Coarse-Grained Simulations of Disordered Proteins and Their Dynamic Interactions.Journal of chemical information and modeling · 2022Article
- Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model.Biomolecules · 2022Article
- Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics.Journal of chemical theory and computation · 2022Article
9 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
A generic coarse-grained (CG) protein model is presented. The intermediate level of resolution (four beads per amino acid, implicit solvent) allows for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic alpha/beta content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. The thermodynamics and kinetics of a three-helix bundle are studied. We check that the CG model is able to fold proteins with tertiary structures and amino acid sequences different from the one used for parameter tuning. By studying both helical and extended conformations we make sure the force field is not biased toward any particular secondary structure. The accuracy involved in folding not only the test protein but also other ones show strong evidence for amino acid cooperativity embedded in the model. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed.
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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.