ArticleJournal of molecular graphics & modelling2016
Visualizing ensembles in structural biology.
Article in Journal of molecular graphics & modelling, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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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
15 citing papers in PubMed, 27 citations in OpenAlex.
- Article
- Simulations suggest double sodium binding induces unexpected conformational changes in thrombin.Journal of molecular modeling · 2022Article
- 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
- Structural characterization of EGFR exon 19 deletion mutation using molecular dynamics simulation.PloS one · 2019Article
- All-atom molecular dynamics comparison of disease-associated zinc fingers.Journal of biomolecular structure & dynamics · 2018Article
- Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin.Journal of biomolecular structure & dynamics · 2017Article
- Mechanistic insights into thrombin's switch between "slow" and "fast" forms.Physical chemistry chemical physics : PCCP · 2017Article
- All-Atom MD Predicts Magnesium-Induced Hairpin in Chemically Perturbed RNA Analog of F10 Therapeutic.The journal of physical chemistry. B · 2017Article
- All-atom MD indicates ion-dependent behavior of therapeutic DNA polymer.Physical chemistry chemical physics : PCCP · 2017Article
- Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins.The journal of physical chemistry. B · 2017Article
- MutSFrontiers in physics · 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
- All-Atom Molecular Dynamics Reveals Mechanism of Zinc Complexation with Therapeutic F10.The journal of physical chemistry. B · 2016Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Displaying a single representative conformation of a biopolymer rather than an ensemble of states mistakenly conveys a static nature rather than the actual dynamic personality of biopolymers. However, there are few apparent options due to the fixed nature of print media. Here we suggest a standardized methodology for visually indicating the distribution width, standard deviation and uncertainty of ensembles of states with little loss of the visual simplicity of displaying a single representative conformation. Of particular note is that the visualization method employed clearly distinguishes between isotropic and anisotropic motion of polymer subunits. We also apply this method to ligand binding, suggesting a way to indicate the expected error in many high throughput docking programs when visualizing the structural spread of the output. We provide several examples in the context of nucleic acids and proteins with particular insights gained via this method. Such examples include investigating a therapeutic polymer of FdUMP (5-fluoro-2-deoxyuridine-5-O-monophosphate) - a topoisomerase-1 (Top1), apoptosis-inducing poison - and nucleotide-binding proteins responsible for ATP hydrolysis from Bacillus subtilis. We also discuss how these methods can be extended to any macromolecular data set with an underlying distribution, including experimental data such as NMR structures.
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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.