ReviewInternational journal of molecular sciences2009
Insights from coarse-grained Gō models for protein folding and dynamics.
Review in International journal of molecular sciences, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
- Coupled Binding and Folding of NS2B/NS3 Protease and Linker Effects Revealed by Topology-Based Modeling.The journal of physical chemistry. B · 2026Article
- Coupled Binding and Folding of NS2B/NS3 Protease and Linker Effects Revealed by Topology-based Modeling.bioRxiv : the preprint server for biology · 2026Article
- Simulating biomolecules for physiological timescales.Current opinion in structural biology · 2025Review
- Thermodynamic coupling of the tandem RRM domains of hnRNP A1 underlie its pleiotropic RNA binding functions.Science advances · 2024Article
- Machine learning meets physics: A two-way street.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Folding kinetics of an entangled protein.PLoS computational biology · 2023Article
- Entangled Motifs in Membrane Protein Structures.International journal of molecular sciences · 2023Article
- Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity.Frontiers in molecular biosciences · 2023Article
- Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma.Biophysics reviews · 2022Review
- Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications.International journal of molecular sciences · 2022Review
- Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions.Frontiers in molecular biosciences · 2022Article
- A Method for Assessing the Robustness of Protein Structures by Randomizing Packing Interactions.Frontiers in molecular biosciences · 2022Article
- Hydrophobic and electrostatic interactions modulate protein escape at the ribosomal exit tunnel.Biophysical journal · 2021Article
- Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions.Biomolecules · 2021Review
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- Unraveling the Coupling between Conformational Changes and Ligand Binding in Ribose Binding Protein Using Multiscale Molecular Dynamics and Free-Energy Calculations.The journal of physical chemistry. B · 2021Article
- A critical perspective on Markov state model treatments of protein-protein association using coarse-grained simulations.The Journal of chemical physics · 2021Article
- From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules.Frontiers in molecular biosciences · 2021Review
- Successes and challenges in simulating the folding of large proteins.The Journal of biological chemistry · 2020Review
- A watershed moment for protein structure prediction.Nature · 2020Article
27 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These include topology-based Gō models, which constitute a smooth and funnel-like approximation to the folding landscape. We review the many variations of the Gō model that have been employed to yield insight into folding mechanisms. Their success has been interpreted as a consequence of the dominant role of the native topology in folding. The role of local contact density in determining protein dynamics is also discussed and is used to explain the ability of Gō-like models to capture sequence effects in folding and elucidate conformational transitions.
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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.