ArticleJournal of chemical theory and computation2023
Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 47 citations in OpenAlex.
- A transfer learning framework for PTP1B inhibitor activity prediction: differential modeling of natural and non-natural products with web platform implementation.Molecular diversity · 2026Article
- ARNy plotter: A comprehensive web server for RNA ensemble structural analysis and visualization.PLoS computational biology · 2026Article
- IDPEnsembleTools: An open-source library for analysis of conformational ensembles of disordered proteins.Protein science : a publication of the Protein Society · 2026Article
- New Approach for Targeting Small-Molecule Candidates for Intrinsically Disordered Proteins.Methods and protocols · 2025Article
- How small molecules stabilize oligomers of a phase-separating disordered protein.bioRxiv : the preprint server for biology · 2025Article
- Structural Plasticity and Functional Dynamics of Pigeon Cryptochrome 4 as Avian Magnetoreceptor.Journal of molecular biology · 2025Article
- Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution.Nature communications · 2025Article
- Targeting protein disorder: the next hurdle in drug discovery.Nature reviews. Drug discovery · 2025Review
- Structural Study of a Peptide Epitope Bearing Multiple Post-Translational Modifications in Rheumatoid Arthritis.International journal of molecular sciences · 2025Article
- Unambiguous assignment of kinked-β sheets leads to insights into molecular grammar of reversibility in biomolecular condensates.Protein science : a publication of the Protein Society · 2025Article
- Energy Landscapes and Structural Plasticity of Intrinsically Disordered Histones.Journal of chemical information and modeling · 2025Article
- Discovery and Characterization of Novel FGFR1 V561M Inhibitors via Virtual Screening and Molecular Dynamics Simulations.ACS medicinal chemistry letters · 2025Article
- Biological insights from integrative modeling of intrinsically disordered protein systems.Current opinion in structural biology · 2025Review
- NeuralTSNE: A Python Package for the Dimensionality Reduction of Molecular Dynamics Data Using Neural Networks.Journal of chemical information and modeling · 2025Article
- Ensemble Docking for Intrinsically Disordered Proteins.Journal of chemical information and modeling · 2025Article
- Covalent Adducts Formed by the Androgen Receptor Transactivation Domain and Small Molecule Drugs Remain Disordered.Journal of chemical information and modeling · 2025Article
- Robustness in biomolecular simulations: Addressing challenges in data generation, analysis, and curation.Cell reports. Physical science · 2025Article
- The ribonucleoprotein hnRNPA1 mediates binding to RNA and DNA telomeric G-quadruplexes through an RGG-rich region.The Journal of biological chemistry · 2025Article
- Ensemble docking for intrinsically disordered proteins.bioRxiv : the preprint server for biology · 2025Article
- PSCP, a novel reactive sulfur donor, activates Keap1-Nrf2 signaling and attenuates mitochondrial dysfunction in diabetic retinopathy.Frontiers in endocrinology · 2025Article
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
Intrinsically disordered proteins (IDPs) populate a range of conformations that are best described by a heterogeneous ensemble. Grouping an IDP ensemble into "structurally similar" clusters for visualization, interpretation, and analysis purposes is a much-desired but formidable task, as the conformational space of IDPs is inherently high-dimensional and reduction techniques often result in ambiguous classifications. Here, we employ the t-distributed stochastic neighbor embedding (t-SNE) technique to generate homogeneous clusters of IDP conformations from the full heterogeneous ensemble. We illustrate the utility of t-SNE by clustering conformations of two disordered proteins, Aβ42, and α-synuclein, in their APO states and when bound to small molecule ligands. Our results shed light on ordered substates within disordered ensembles and provide structural and mechanistic insights into binding modes that confer specificity and affinity in IDP ligand binding. t-SNE projections preserve the local neighborhood information, provide interpretable visualizations of the conformational heterogeneity within each ensemble, and enable the quantification of cluster populations and their relative shifts upon ligand binding. Our approach provides a new framework for detailed investigations of the thermodynamics and kinetics of IDP ligand binding and will aid rational drug design for IDPs.
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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.