ArticleProteins2008
A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding.
Article in Proteins, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Mapping Still Matters: Coarse-Graining with Machine Learning Potentials.Journal of chemical information and modeling · 2026Article
- Artificially intelligent modeling of macromolecular assemblies.Frontiers in molecular biosciences · 2026Review
- Detecting intermediate protein conformations using algebraic topology.BMC bioinformatics · 2017Article
- Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics.Journal of molecular modeling · 2013Article
- Improvement of structure-based potentials for protein folding by native and nonnative hydrogen bonds.Biophysical journal · 2011Article
- Constraining local structure can speed up folding by promoting structural polarization of the folding pathway.Protein science : a publication of the Protein Society · 2011Article
- MSCALE: A General Utility for Multiscale Modeling.Journal of chemical theory and computation · 2011Article
- Multiscale coarse-graining of the protein energy landscape.PLoS computational biology · 2010Article
- A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins.Proteins · 2009Article
- A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids.Journal of chemical theory and computation · 2009Article
- Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field.Proteins · 2009Article
- Generic coarse-grained model for protein folding and aggregation.The Journal of chemical physics · 2009Article
- Insights from coarse-grained Gō models for protein folding and dynamics.International journal of molecular sciences · 2009Review
- Contrasting disease and nondisease protein aggregation by molecular simulation.Accounts of chemical research · 2008Review
- Protofibril assemblies of the arctic, Dutch, and Flemish mutants of the Alzheimer's Abeta1-40 peptide.Biophysical journal · 2008Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We develop a sequence based alpha-carbon model to incorporate a mean field estimate of the orientation dependence of the polypeptide chain that gives rise to specific hydrogen bond pairing to stabilize alpha-helices and beta-sheets. We illustrate the success of the new protein model in capturing thermodynamic measures and folding mechanism of proteins L and G. Compared to our previous coarse-grained model, the new model shows greater folding cooperativity and improvements in designability of protein sequences, as well as predicting correct trends for kinetic rates and mechanism for proteins L and G. We believe the model is broadly applicable to other protein folding and protein-protein co-assembly processes, and does not require experimental input beyond the topology description of the native state. Even without tertiary topology information, it can also serve as a mid-resolution protein model for more exhaustive conformational search strategies that can bridge back down to atomic descriptions of the polypeptide chain.
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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.