ArticleJournal of chemical theory and computation2009
A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids.
Article in Journal of chemical theory and computation, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- CGsmiles: A Versatile Line Notation for Molecular Representations across Multiple Resolutions.Journal of chemical information and modeling · 2025Article
- Unraveling protein's structural dynamics: from configurational dynamics to ensemble switching guides functional mesoscale assemblies.Current opinion in structural biology · 2021Review
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- Molecular dynamics simulations in photosynthesis.Photosynthesis research · 2020Review
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- Coarse-grained molecular dynamics studies of the structure and stability of peptide-based drug amphiphile filaments.Soft matter · 2017Article
- Molecular simulations of peptide amphiphiles.Organic & biomolecular chemistry · 2017Review
- The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.Chemical Society reviews · 2014Review
- Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices.Journal of chemical theory and computation · 2014Article
- Molecular mechanics.Current pharmaceutical design · 2014Review
- A generic force field for protein coarse-grained molecular dynamics simulation.International journal of molecular sciences · 2012Article
- Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides.Journal of chemical theory and computation · 2012Article
- Molecular dynamics simulations of voltage-gated cation channels: insights on voltage-sensor domain function and modulation.Frontiers in pharmacology · 2012Article
- Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models.Journal of computer-aided molecular design · 2011Article
- Protein folding pathways and state transitions described by classical equations of motion of an elastic network model.Protein science : a publication of the Protein Society · 2010Article
- Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration.The Journal of chemical physics · 2010Article
- Multiscale coarse-graining of the protein energy landscape.PLoS computational biology · 2010Article
- Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field.The journal of physical chemistry. B · 2010Article
- Article
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Authors and funding
4 authors.
Funding
Abstract
The large quantity of protein sequences being generated from genomic data has greatly outpaced the throughput of experimental protein structure determining methods and consequently brought urgency to the need for accurate protein structure prediction tools. Reduced resolution, or coarse grained (CG) models, have become a mainstay in computational protein structure prediction perfoming among the best tools available. The quest for high quality generalized CG models presents an extremely challenging yet popular endeavor. To this point, a CG based interaction potential is presented here for the naturally occurring amino acids. In the present approach, three to four heavy atoms and associated hydrogens are condensed into a single CG site. The parameterization of the site-site interaction potential relies on experimental data thus providing a novel approach that is neither based on all-atom (AA) simulations nor experimental protein structural data. Specifically, intermolecular potentials, which are based on Lennard-Jones (LJ) style functional forms, are parameterized using thermodynamic data including surface tension and density. Using this approach, an amino acid potential dataset has been developed for use in modeling peptides and proteins. The potential is evaluated here by comparing the solvent accessible surface area (SASA) to AA representations and ranking of protein decoy data sets provided by Decoys 'R' Us. The model is shown to perform very well compared to other existing prediction models for these properties.
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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.