ArticleBiophysical journal2020
Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins.
Article in Biophysical journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Toward a unified framework for determining conformational ensembles of disordered proteins.Nature methods · 2026Review
- Targeting protein disorder: the next hurdle in drug discovery.Nature reviews. Drug discovery · 2025Review
- Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis.Journal of chemical theory and computation · 2025Article
- Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution.Journal of chemical information and modeling · 2024Article
- Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins.Bioinformatics (Oxford, England) · 2024Article
- Protein ensemble modeling and analysis with MMMx.Protein science : a publication of the Protein Society · 2024Article
- PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins.Nucleic acids research · 2024Article
- Characterization of Intrinsically Disordered Proteins in Healthy and Diseased States by Nuclear Magnetic Resonance.Reviews on recent clinical trials · 2024Review
- The Entamoeba histolytica Vps26 (EhVps26) retromeric protein is involved in phagocytosis: Bioinformatic and experimental approaches.PloS one · 2024Article
- Analysis of Structural Changes in the Protein near the Phosphorylation Site.Biomolecules · 2023Article
- Delineating Structural Propensities of the 4E-BP2 Protein via Integrative Modeling and Clustering.The journal of physical chemistry. B · 2023Article
- Another pearl in the "copper-transport" necklace.Biophysical journal · 2021Article
- When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes.Biomolecules · 2021Review
- Folding and self-assembly of short intrinsically disordered peptides and protein regions.Nanoscale advances · 2021Review
- PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.Nucleic acids research · 2021Article
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Authors and funding
6 authors.
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Abstract
Intrinsically disordered proteins are proteins whose native functional states represent ensembles of highly diverse conformations. Such ensembles are a challenge for quantitative structure comparisons because their conformational diversity precludes optimal superimposition of the atomic coordinates necessary for deriving common similarity measures such as the root mean-square deviation of these coordinates. Here, we introduce superimposition-free metrics that are based on computing matrices of the Cα-Cα distance distributions within ensembles and comparing these matrices between ensembles. Differences between two matrices yield information on the similarity between specific regions of the polypeptide, whereas the global structural similarity is captured by the root mean-square difference between the medians of the Cα-Cα distance distributions of two ensembles. Together, our metrics enable rigorous investigations of structure-function relationships in conformational ensembles of intrinsically disordered proteins derived using experimental restraints or by molecular simulations and for proteins containing both structured and disordered regions.
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