ArticleJournal of chemical theory and computation2017
Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.
Article in Journal of chemical theory and computation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Challenges and opportunities in computational studies for lipid nanoparticle development.npj drug discovery · 2025Review
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050.ACS physical chemistry Au · 2024Review
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Simulations of Functional Motions of Super Large Biomolecules with a Mixed-Resolution Model.Journal of chemical theory and computation · 2024Article
- Enhanced Drug Uptake on Application of Electroporation in a Single-Cell Model.The Journal of membrane biology · 2023Article
- Coarse-grained (hybrid) integrative modeling of biomolecular interactions.Computational and structural biotechnology journal · 2020Review
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.Interface focus · 2019Review
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- Emerging Diversity in Lipid-Protein Interactions.Chemical reviews · 2019Review
- CABS-flex standalone: a simulation environment for fast modeling of protein flexibility.Bioinformatics (Oxford, England) · 2019Article
- Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α.PloS one · 2019Article
- Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology.The Journal of membrane biology · 2018Review
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
- Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments.Chemical Society reviews · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Hybrid all-atom/coarse-grained (AA/CG) simulations of proteins offer a computationally efficient compromise where atomistic details are only applied to biologically relevant regions while benefiting from the speedup of treating the remaining parts of a given system at the CG level. The recently developed CG model, PRIMO, allows a direct coupling with an atomistic force field with no additional modifications or coupling terms and the ability to carry out dynamic simulations without any restraints on secondary or tertiary structures. A hybrid AA/CG scheme based on combining all-atom CHARMM and coarse-grained PRIMO representations was validated via molecular dynamics and replica exchange simulations of soluble and membrane proteins. The AA/CG scheme was also tested in the calculation of the free energy profile for the transition from the closed to the open state of adenylate kinase via umbrella sampling molecular dynamics method. The overall finding is that the AA/CG scheme generates dynamics and energetics that are qualitatively and quantitatively comparable to AA simulations while offering the computational advantages of coarse-graining. This model opens the door to challenging applications where high accuracy is required only in parts of large biomolecular complexes.
Indexed as
Identifiers
What OpenQuestion holds
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.