ReviewThe protein journal2023
A Retrospective on the Development of Methods for the Analysis of Protein Conformational Ensembles.
Review in The protein journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Repurposing of natural products for spinocerebellar ataxia type 3 using integrated network pharmacology and in silico approaches.Scientific reports · 2026Article
- Structural and thermodynamic impact of oncogenic mutations on the nucleosome core particle.Biophysical journal · 2025Article
- Protein domain movement involved in binding of belinostat and HPOB as inhibitors of histone deacetylase 6 (HDAC6): a hybrid automated-interactive docking study.Journal of computer-aided molecular design · 2025Article
- Complementing Adiabatic and Nonadiabatic Methods To Understand Internal Conversion Dynamics in Porphyrin Derivatives.Journal of chemical theory and computation · 2024Article
- Phytoconstituents of Withania somnifera (L.) Dunal (Ashwagandha) unveiled potential cerebroside sulfotransferase inhibitors: insight through virtual screening, molecular dynamics, toxicity, and reverse pharmacophore analysis.Journal of biological engineering · 2024Article
- Multilevel superposition for deciphering the conformational variability of protein ensembles.Briefings in bioinformatics · 2024Article
- Article
- Article
- Predictive identification and design of potent inhibitors targeting resistance-inducing candidate genes fromFrontiers in bioinformatics · 2024Article
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Authors and funding
1 author.
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Abstract
Analysing protein conformational ensembles whether from molecular dynamics (MD) simulation or other sources for functionally relevant conformational changes can be very challenging. In the nineteen nineties dimensional reduction methods were developed primarily for analysing MD trajectories to determine dominant motions with the aim of understanding their relationship to function. Coarse-graining methods were also developed so the conformational change between two structures could be described in terms of the relative motion of a small number of quasi-rigid regions rather than in terms of a large number of atoms. When these methods are combined, they can characterize the large-scale motions inherent in a conformational ensemble providing insight into possible functional mechanism. The dimensional reduction methods first applied to protein conformational ensembles were referred to as Quasi-Harmonic Analysis, Principal Component Analysis and Essential Dynamics Analysis. A retrospective on the origin of these methods is presented, the relationships between them explained, and more recent developments reviewed.
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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.