ReviewAdvances in protein chemistry and structural biology2014
Recent advances in transferable coarse-grained modeling of proteins.
Review in Advances in protein chemistry and structural biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- MOFF2: A Transferable Coarse-Grained Protein Force Field for Predictive Condensate Simulations.bioRxiv : the preprint server for biology · 2026Article
- Navigating protein landscapes with a machine-learned transferable coarse-grained model.Nature chemistry · 2025Article
- COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins.Journal of chemical theory and computation · 2025Article
- COCOMO2: A coarse-grained model for interacting folded and disordered proteins.bioRxiv : the preprint server for biology · 2024Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Insertion and Anchoring of HIV-1 Fusion Peptide into Complex Membrane Mimicking Human T-cell.bioRxiv : the preprint server for biology · 2024Article
- One bead per residue can describe all-atom protein structures.Structure (London, England : 1993) · 2024Article
- Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks.ACS central science · 2023Article
- Transferable Coarse Graining via Contrastive Learning of Graph Neural Networks.bioRxiv : the preprint server for biology · 2023Article
- Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining.Journal of chemical information and modeling · 2023Article
- Modeling Concentration-dependent Phase Separation Processes Involving Peptides and RNA via Residue-Based Coarse-Graining.Journal of chemical theory and computation · 2023Article
- Unifying coarse-grained force fields for folded and disordered proteins.Current opinion in structural biology · 2022Review
- Review
- Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review.Journal of chemical information and modeling · 2021Review
- Association Mechanism of Peptide-Coated Metal Nanoparticles with Model Membranes: A Coarse-Grained Study.Journal of chemical theory and computation · 2021Article
- Article
- Consistent Force Field Captures Homologue-Resolved HP1 Phase Separation.Journal of chemical theory and computation · 2021Article
- Temperature and Phase Transferable Bottom-up Coarse-Grained Models.Journal of chemical theory and computation · 2020Article
- Brownian Dynamics Simulations of Biological Molecules.Trends in chemistry · 2019Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Computer simulations are indispensable tools for studying the structure and dynamics of biological macromolecules. Biochemical processes occur on different scales of length and time. Atomistic simulations cannot cover the relevant spatiotemporal scales at which the cellular processes occur. To address this challenge, coarse-grained (CG) modeling of the biological systems is employed. Over the last few years, many CG models for proteins continue to be developed. However, many of them are not transferable with respect to different systems and different environments. In this review, we discuss those CG protein models that are transferable and that retain chemical specificity. We restrict ourselves to CG models of soluble proteins only. We also briefly review recent progress made in the multiscale hybrid all-atom/CG simulations of proteins.
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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.