ArticleNature physics2010
Challenges in protein folding simulations: Timescale, representation, and analysis.
Article in Nature physics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers.
What it found
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Who cites it
110 citing papers in PubMed.
- Developing and Benchmarking Sage 2.3.0 with the AshGC Neural Network Charge Model.Journal of chemical theory and computation · 2026Article
- Unavailability of experimental 3D structural data on protein folding dynamics and necessity for a new generation of structure prediction methods in this context.Bioinformatics (Oxford, England) · 2026Article
- Accelerating Replica Exchange Molecular Dynamics: A Comparison of Hydrogen Mass Repartitioning and Light Water Models.Journal of chemical theory and computation · 2026Article
- BioEmu: AI-Powered Revolution in Scalable Protein Dynamics Simulation.Journal of cellular and molecular medicine · 2025Article
- FINCHES: A Computational Framework for Predicting Intermolecular Interactions in Intrinsically Disordered Proteins.International journal of molecular sciences · 2025Review
- GōMartini 3: From large conformational changes in proteins to environmental bias corrections.Nature communications · 2025Article
- Structure and dynamics in drug discovery.npj drug discovery · 2024Review
- The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics.Journal of chemical theory and computation · 2024Article
- Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations.Journal of chemical theory and computation · 2023Article
- Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations.Journal of chemical information and modeling · 2023Article
- Unveiling Switching Function of Amino Acids in Proteins Using a Machine Learning Approach.Journal of chemical theory and computation · 2023Article
- Pathfinder: Protein folding pathway prediction based on conformational sampling.PLoS computational biology · 2023Article
- A Study of a Protein-Folding Machine: Transient Rotation of the Polypeptide Backbone Facilitates Rapid Folding of Protein Domains in All-Atom Molecular Dynamics Simulations.International journal of molecular sciences · 2023Article
- Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions.Molecules (Basel, Switzerland) · 2022Review
- Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.The journal of physical chemistry. B · 2022Article
- Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics.Journal of chemical theory and computation · 2022Article
- Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes.Advanced drug delivery reviews · 2022Review
- Crystal-structures-guided design of fragment-based drugs for inhibiting the main protease of SARS-CoV-2.Proteins · 2022Article
- Accelerating Protein Folding Molecular Dynamics Using Inter-Residue Distances from Machine Learning Servers.Journal of chemical theory and computation · 2022Article
- Granger Causality Analysis of Chignolin Folding.Journal of chemical theory and computation · 2022Article
50 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Experimental studies of protein folding processes are frequently hampered by the fact that only low resolution structural data can be obtained with sufficient temporal resolution. Molecular dynamics simulations offer a complementary approach, providing extremely high resolution spatial and temporal data on folding processes. The effectiveness of such simulations is currently hampered by continuing questions regarding the ability of molecular dynamics force fields to reproduce the true potential energy surfaces of proteins, and ongoing difficulties with obtaining sufficient sampling to meaningfully comment on folding mechanisms. We review recent progress in the simulation of three common model systems for protein folding, and discuss how recent advances in technology and theory are allowing protein folding simulations to address their current shortcomings.
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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.