ArticleBiophysical journal2009
Force field bias in protein folding simulations.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
What it found
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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.
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Who cites it
75 citing papers in PubMed, 195 citations in OpenAlex.
- Multiscale Neural Network Potential with Anisotropic Message Passing for the Fast and Accurate Simulation of Protein Dynamics and Enzymatic Reactions.Journal of the American Chemical Society · 2026Article
- Proteins Inside the HSP60/HSP10 Fold Under a Constant Electric Field: Potential Implications for the Protein Folding Problem.International journal of molecular sciences · 2026Article
- Prediction and biological significance of small changes in binding of leiomodin to tropomyosin.The Journal of general physiology · 2025Article
- Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens.Nature communications · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Intrinsic disorder and conformational coexistence in auxin coreceptors.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Gaussian Process Regression Models for Predicting Atomic Energies and Multipole Moments.Journal of chemical theory and computation · 2023Article
- Computational Models for the Study of Protein Aggregation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Length Dependent Folding Kinetics of Alanine-Based Helical Peptides from Optimal Dimensionality Reduction.Life (Basel, Switzerland) · 2021Article
- DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics.Nucleic acids research · 2021Article
- Exploration of the Misfolding Mechanism of Transthyretin Monomer: Insights from Hybrid-Resolution Simulations and Markov State Model Analysis.Biomolecules · 2019Article
- Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins.Biophysical journal · 2019Review
- Computational Estimation of Microsecond to Second Atomistic Folding Times.Journal of the American Chemical Society · 2019Article
- Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.Journal of computer-aided molecular design · 2019Review
- Accurate Biomolecular Simulations Account for Electronic Polarization.Frontiers in molecular biosciences · 2019Article
- Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins.Computational and structural biotechnology journal · 2019Review
- Folding Molecular Dynamics Simulation of a gp41-Derived Peptide Reconcile Divergent Structure Determinations.ACS omega · 2018Article
- A spin-1 representation for dual-funnel energy landscapes.The Journal of chemical physics · 2018Article
- Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes.The journal of physical chemistry. B · 2017Article
- Conformations of a Metastable SH3 Domain Characterized by smFRET and an Excluded-Volume Polymer Model.Biophysical journal · 2016Article
15 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Long timescale (>1 micros) molecular dynamics simulations of protein folding offer a powerful tool for understanding the atomic-scale interactions that determine a protein's folding pathway and stabilize its native state. Unfortunately, when the simulated protein fails to fold, it is often unclear whether the failure is due to a deficiency in the underlying force fields or simply a lack of sufficient simulation time. We examine one such case, the human Pin1 WW domain, using the recently developed deactivated morphing method to calculate free energy differences between misfolded and folded states. We find that the force field we used favors the misfolded states, explaining the failure of the folding simulations. Possible further applications of deactivated morphing and implications for force field development are discussed.
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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.