ArticleJournal of biomolecular structure & dynamics2016
Importance of long-time simulations for rare event sampling in zinc finger proteins.
Article in Journal of biomolecular structure & dynamics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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.
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.
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Who cites it
12 citing papers in PubMed.
- Article
- Simulations suggest double sodium binding induces unexpected conformational changes in thrombin.Journal of molecular modeling · 2022Article
- High five! Methyl probes at five ring positions of phenylalanine explore the hydrophobic core dynamics of zinc finger miniproteins.Chemical science · 2021Article
- Light Chain Mutation Effects on the Dynamics of Thrombin.Journal of chemical information and modeling · 2021Article
- Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning.Journal of biomolecular structure & dynamics · 2019Article
- Using correlated motions to determine sufficient sampling times for molecular dynamics.Physical review. E · 2018Article
- All-atom molecular dynamics comparison of disease-associated zinc fingers.Journal of biomolecular structure & dynamics · 2018Article
- Visualizing correlated motion with HDBSCAN clustering.Protein science : a publication of the Protein Society · 2018Article
- Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin.Journal of biomolecular structure & dynamics · 2017Article
- Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator).Biochemistry · 2017Article
- Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge.Journal of chemical theory and computation · 2016Article
- Visualizing ensembles in structural biology.Journal of molecular graphics & modelling · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Molecular dynamics (MD) simulation methods have seen significant improvement since their inception in the late 1950s. Constraints of simulation size and duration that once impeded the field have lessened with the advent of better algorithms, faster processors, and parallel computing. With newer techniques and hardware available, MD simulations of more biologically relevant timescales can now sample a broader range of conformational and dynamical changes including rare events. One concern in the literature has been under which circumstances it is sufficient to perform many shorter timescale simulations and under which circumstances fewer longer simulations are necessary. Herein, our simulations of the zinc finger NEMO (2JVX) using multiple simulations of length 15, 30, 1000, and 3000 ns are analyzed to provide clarity on this point.
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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.