ReviewMolecules (Basel, Switzerland)2019
Normal Mode Analysis as a Routine Part of a Structural Investigation.
Review in Molecules (Basel, Switzerland), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Adaptive Normal Mode Sampling (aMDeNM) Enhances Exploration of Protein Conformational Space and Reveals the Functional Role of Frequency Coupling.Journal of chemical theory and computation · 2026Article
- Structural Features of a Tiny Viral Protein, ORF7b of SARS-CoV-2.International journal of molecular sciences · 2026Article
- mRNA vaccine design targeting Merkel cell polyomavirus for immunotherapy of Merkel cell carcinoma.Scientific reports · 2026Article
- A comparative in silico and in vitro analysis of antiviral agents targeting estrogen and progesterone receptors in breast cancer.Scientific reports · 2026Article
- Sanguinarine and Doxorubicin Inhibit Heat Shock Protein HSPA5 and Trigger ER Stress in Breast Cancer.Cell biochemistry and biophysics · 2026Article
- Catechins as antibiofilm agents: molecular insights for virtual screening and inFrontiers in pharmacology · 2026Article
- Molecular Basis for Vacuolar Iron Transport by OsVIT2, a Target for Iron Biofortification in Rice.Proteins · 2025Article
- In Silico Development of a Chimeric Multi-Epitope Vaccine TargetingPharmaceuticals (Basel, Switzerland) · 2025Article
- Decoding allosteric landscapes: computational methodologies for enzyme modulation and drug discovery.RSC chemical biology · 2025Review
- Conformational Dynamics of Mitochondrial Inorganic Pyrophosphatase hPPA2 and Its Changes Caused by Pathogenic Mutations.Life (Basel, Switzerland) · 2025Article
- Computational analysis of the structural-functional dynamics of a Co-receptor proteoglycan.Frontiers in molecular biosciences · 2025Article
- Hyperthermophilic xylanase and thermophilicity analysis by molecular dynamic simulation with quantum mechanics.Applied microbiology and biotechnology · 2024Article
- ATOMDANCE: Kernel-based denoising and choreographic analysis for protein dynamic comparison.Biophysical journal · 2024Article
- Structural shifts in TolC facilitate Efflux-Mediated β-lactam resistance.Communications biology · 2024Article
- AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Nucleocapsid Protein Variants.Viruses · 2024Article
- Insights into mechanisms of MALT1 allostery from NMR and AlphaFold dynamic analyses.Communications biology · 2024Article
- A Fresh Look at the Normal Mode Analysis of Proteins: Introducing Allosteric Co-Vibrational Modes.JACS Au · 2024Article
- Integrative approaches for characterizing protein dynamics: NMR, CryoEM, and computer simulations.Current opinion in structural biology · 2024Review
- A perspective on the sharing of docking data.Data in brief · 2023Article
- H-Bonds in Crambin: Coherence in an α-Helix.ACS omega · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Normal mode analysis (NMA) is a technique that can be used to describe the flexible states accessible to a protein about an equilibrium position. These states have been shown repeatedly to have functional significance. NMA is probably the least computationally expensive method for studying the dynamics of macromolecules, and advances in computer technology and algorithms for calculating normal modes over the last 20 years have made it nearly trivial for all but the largest systems. Despite this, it is still uncommon for NMA to be used as a component of the analysis of a structural study. In this review, we will describe NMA, outline its advantages and limitations, explain what can and cannot be learned from it, and address some criticisms and concerns that have been voiced about it. We will then review the most commonly used techniques for reducing the computational cost of this method and identify the web services making use of these methods. We will illustrate several of their possible uses with recent examples from the literature. We conclude by recommending that NMA become one of the standard tools employed in any structural study.
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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.