ArticleScientific reports2013
A coarse-grained protein model in a water-like solvent.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Hydration Free Energies of Linear Alkanes: Systematic Deviations in Common Water Models and Their Correction.The journal of physical chemistry. B · 2026Article
- Context Dependency of Hydrophobicity in Intrinsically Disordered Proteins: Insights from a New Dewetting Free Energy-Based Hydrophobicity Scale.The journal of physical chemistry. B · 2025Article
- Data-Driven Methods for Accelerating Polymer Design.ACS polymers Au · 2022Review
- Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures.Nature reviews. Chemistry · 2018Article
- Synthetic, Switchable Enzymes.Journal of molecular microbiology and biotechnology · 2017Review
- The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.Chemical Society reviews · 2014Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Simulations employing an explicit atom description of proteins in solvent can be computationally expensive. On the other hand, coarse-grained protein models in implicit solvent miss essential features of the hydrophobic effect, especially its temperature dependence, and have limited ability to capture the kinetics of protein folding. We propose a free space two-letter protein ("H-P") model in a simple, but qualitatively accurate description for water, the Jagla model, which coarse-grains water into an isotropically interacting sphere. Using Monte Carlo simulations, we design protein-like sequences that can undergo a collapse, exposing the "Jagla-philic" monomers to the solvent, while maintaining a "hydrophobic" core. This protein-like model manifests heat and cold denaturation in a manner that is reminiscent of proteins. While this protein-like model lacks the details that would introduce secondary structure formation, we believe that these ideas represent a first step in developing a useful, but computationally expedient, means of modeling proteins.
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Registered trials
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