ArticlePloS one2018
Protein dynamic communities from elastic network models align closely to the communities defined by molecular dynamics.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed, 57 citations in OpenAlex.
- Network analysis of correlated conformational dynamics across the evolution of influenza A virus NS1.bioRxiv : the preprint server for biology · 2026Article
- Elucidating HER2-directed chimeric antigen receptor (CAR) activation mechanism using homology modeling and all-atom molecular dynamics simulation.Computational and structural biotechnology journal · 2026Article
- Exploring the Hemoglobin T to R2 Path Using Gaussian Elastic Network Correlation Map Distance.Proteins · 2025Article
- A protein dynamics-based deep learning model enhances predictions of fitness and epistasis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Impact of Bile Acid Amidation on In Silico Farnesoid X Receptor Dynamics.The journal of physical chemistry. B · 2025Article
- Dynamics-based protein network features accurately discriminate neutral and rheostat positions.Biophysical journal · 2024Article
- Differential network analysis reveals the key role of the ECM-receptor pathway inMolecular therapy. Nucleic acids · 2024Article
- Reused Protein Segments Linked to Functional Dynamics.Molecular biology and evolution · 2024Article
- Investigating Pyruvate Dehydrogenase Kinase 3 Inhibitory Potential of Myricetin Using Integrated Computational and Spectroscopic Approaches.ACS omega · 2024Article
- Article
- Article
- Insight into the Nucleotide Based Modulation of the Grp94 Molecular Chaperone Using Multiscale Dynamics.The journal of physical chemistry. B · 2023Article
- Predicting allosteric pockets in protein biological assemblages.Bioinformatics (Oxford, England) · 2023Article
- Article
- Mechanistic insight into impact of phosphorylation on the enzymatic steps of farnesyltransferase.Protein science : a publication of the Protein Society · 2022Article
- PSP-GNM: Predicting Protein Stability Changes upon Point Mutations with a Gaussian Network Model.International journal of molecular sciences · 2022Article
- Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier.Bioinformatics (Oxford, England) · 2022Article
- Identification of Phytoconstituents as Potent Inhibitors of Casein Kinase-1 Alpha Using Virtual Screening and Molecular Dynamics Simulations.Pharmaceutics · 2021Article
- LARGE-SCALE MULTIPLE INFERENCE OF COLLECTIVE DEPENDENCE WITH APPLICATIONS TO PROTEIN FUNCTION.The annals of applied statistics · 2021Article
- Structural Determination, Biological Function, and Molecular Modelling Studies of Sulfoaildenafil Adulterated in Herbal Dietary Supplement.Molecules (Basel, Switzerland) · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Dynamic communities in proteins comprise the cohesive structural units that individually exhibit rigid body motions. These can correspond to structural domains, but are usually smaller parts that move with respect to one another in a protein's internal motions, key to its functional dynamics. Previous studies emphasized their importance to understand the nature of ligand-induced allosteric regulation. These studies reported that mutations to key community residues can hinder transmission of allosteric signals among the communities. Usually molecular dynamic (MD) simulations (~ 100 ns or longer) have been used to identify the communities-a demanding task for larger proteins. In the present study, we propose that dynamic communities obtained from MD simulations can also be obtained alternatively with simpler models-the elastic network models (ENMs). To verify this premise, we compare the specific communities obtained from MD and ENMs for 44 proteins. We evaluate the correspondence in communities from the two methods and compute the extent of agreement in the dynamic cross-correlation data used for community detection. Our study reveals a strong correspondence between the communities from MD and ENM and also good agreement for the residue cross-correlations. Importantly, we observe that the dynamic communities from MD can be closely reproduced with ENMs. With ENMs, we also compare the community structures of stable and unstable mutant forms of T4 Lysozyme with its wild-type. We find that communities for unstable mutants show substantially poorer agreement with the wild-type communities than do stable mutants, suggesting such ENM-based community structures can serve as a means to rapidly identify deleterious mutants.
Indexed as
Identifiers
What OpenQuestion holds
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.