ArticleProtein science : a publication of the Protein Society2024
Protein ensemble modeling and analysis with MMMx.
Article in Protein science : a publication of the Protein Society, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- EPR spectroscopy 80 years after its discovery.Science advances · 2026Review
- Beyond a Passive Tether: Structural Insights into the Disordered Tail of Hsp90.Journal of the American Chemical Society · 2026Article
- Characterization of flexible RNA binding by tandem RNA recognition motifs through integrative ensemble modelling.Nucleic acids research · 2026Article
- IDPEnsembleTools: An open-source library for analysis of conformational ensembles of disordered proteins.Protein science : a publication of the Protein Society · 2026Article
- Recent advances in quantifying protein conformational ensembles with dipolar EPR spectroscopy.Current opinion in structural biology · 2025Review
- Modeling protein conformational ensembles by guiding AlphaFold2 with Double Electron Electron Resonance (DEER) distance distributions.Nature communications · 2025Article
- Protein Modeling with DEER Spectroscopy.Annual review of biophysics · 2025Review
- Protein ensemble modeling and analysis with MMMx.Protein science : a publication of the Protein Society · 2024Article
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Authors and funding
1 author.
Funding
Abstract
Proteins, especially of eukaryotes, often have disordered domains and may contain multiple folded domains whose relative spatial arrangement is distributed. The MMMx ensemble modeling and analysis toolbox (https://github.com/gjeschke/MMMx) can support the design of experiments to characterize the distributed structure of such proteins, starting from AlphaFold2 predictions or folded domain structures. Weak order can be analyzed with reference to a random coil model or to peptide chains that match the residue-specific Ramachandran angle distribution of the loop regions and are otherwise unrestrained. The deviation of the mean square end-to-end distance of chain sections from their average over sections of the same sequence length reveals localized compaction or expansion of the chain. The shape sampled by disordered chains is visualized by superposition in the principal axes frame of their inertia tensor. Ensembles of different sizes and with weighted conformers can be compared based on a similarity parameter that abstracts from the ensemble width.
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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.