ArticleThe journal of physical chemistry. B2016
Rapid Characterization of Allosteric Networks with Ensemble Normal Mode Analysis.
Article in The journal of physical chemistry. B, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 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
32 citing papers in PubMed, 70 citations in OpenAlex.
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- Global comparative structural analysis of responses to protein phosphorylation.Nature communications · 2025Article
- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
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- Illuminating Protein Allostery by Chemically Accurate Contact Response Analysis (ChACRA).Journal of chemical theory and computation · 2024Article
- MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search.Journal of chemical information and modeling · 2024Article
- Article
- An Assessment of Quaternary Structure Functionality in Homomer Protein Complexes.Molecular biology and evolution · 2023Article
- The "violin model": Looking at community networks for dynamic allostery.The Journal of chemical physics · 2023Review
- Developmental landscape of computational techniques to explore the potential phytochemicals fromFrontiers in molecular biosciences · 2023Article
- Explicit versus implicit consideration of binding partners in protein-protein complex to elucidate intrinsic dynamics.Biophysical reviews · 2022Review
- Molecular Docking and Molecular Dynamics Studies Reveal Secretory Proteins as Novel Targets of Temozolomide in Glioblastoma Multiforme.Molecules (Basel, Switzerland) · 2022Article
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Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
Allosteric regulation is a primary means of controlling protein function. By definition, allostery involves the propagation of structural dynamic changes between distal protein sites that yields a functional change. Gaining improved knowledge of these fundamental mechanisms is important for understanding many biomolecular processes and for guiding protein engineering and drug design efforts. In this work we compare and contrast a range of normal mode analysis (NMA) approaches together with network analysis for the prediction of structural dynamics and allosteric sites. Application to heterotrimeric G proteins, hemoglobin, and caspase 7 indicates that atomistic elastic network models provide improved predictions of experimental allosteric mutation sites. Results for G proteins also display an improved consistency with those derived from more computationally demanding MD simulations. Application of this approach across available experimental structures for a given protein family in a unified manner, that we refer to as ensemble NMA, yields the best overall predictive performance. We propose that this atomistic ensemble NMA approach represents an efficient and powerful tool for guiding the exploration of coupled motions and allosteric mechanisms in cases where multiple structures are available and where MD may prove prohibitively expensive.
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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.