ArticleJournal of chemical theory and computation2013
PRIMO: A Transferable Coarse-grained Force Field for Proteins.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Accurate interdomain contacts in a mixed folded protein from NMR-guided coarse-grained simulations.Physical chemistry chemical physics : PCCP · 2026Article
- AMARO: All Heavy-Atom Transferable Neural Network Potentials of Protein Thermodynamics.Journal of chemical theory and computation · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Evaluation of Essential Dynamics and Fixed-Length Coarse Graining for Multidomain Proteins.The journal of physical chemistry. B · 2024Article
- Simulations of Functional Motions of Super Large Biomolecules with a Mixed-Resolution Model.Journal of chemical theory and computation · 2024Article
- Organizations of melittin peptides after spontaneous penetration into cell membranes.Biophysical journal · 2022Article
- Effect of Disulfide Bridge on the Binding of SARS-CoV-2 Fusion Peptide to Cell Membrane: A Coarse-Grained Study.ACS omega · 2022Article
- Bottom-up Coarse-Graining: Principles and Perspectives.Journal of chemical theory and computation · 2022Review
- Applications of Molecular Dynamics Simulation in Protein Study.Membranes · 2022Review
- Computational Models for the Study of Protein Aggregation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Accurate Description of Protein-Protein Recognition and Protein Aggregation with the Implicit-Solvent-Based PACSAB Protein Model.Polymers · 2021Article
- Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps.Journal of chemical information and modeling · 2021Article
- Temperature and Phase Transferable Bottom-up Coarse-Grained Models.Journal of chemical theory and computation · 2020Article
- Ligand-protein interactions in lysozyme investigated through a dual-resolution model.Proteins · 2020Article
- Computational Nanoscopy of Tight Junctions at the Blood-Brain Barrier Interface.International journal of molecular sciences · 2019Review
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications.International journal of molecular sciences · 2019Review
- A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model.The Journal of chemical physics · 2019Article
- Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.Chemical reviews · 2019Review
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
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5 authors.
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Abstract
We describe here the PRIMO (PRotein Intermediate Model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multi-scale simulations. The energy function consists of standard molecular dynamics energy terms plus a hydrogen-bonding potential term and is mainly parameterized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent is treated implicitly via the generalized Born model. The bonded interactions are either harmonic or distance-based spline interpolated potentials. These potentials are defined on the basis of all-atom molecular dynamics (MD) simulations of dipeptides with the CHARMM22/CMAP force field. The non-bonded parameters are tuned by matching conformational free energies of diverse set of conformations with that of CHARMM all-atom results. PRIMO is designed to provide a correct description of conformational distribution of the backbone (ϕ/ψ) and side chains (χ
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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.