ArticleJournal of chemical theory and computation2025
Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins Reveal Asymmetric Chain Compaction.
Article in Journal of chemical theory and computation, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.Journal of chemical theory and computation · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.ArXiv · 2026Article
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Authors and funding
2 authors.
Funding
Abstract
Intrinsically disordered proteins (IDPs) exhibit highly dynamic and heterogeneous conformational ensembles that are strongly influenced by sequence features. While global properties such as chain compaction and scaling behavior have been widely studied, they often fail to resolve the fine-grained, sequence-specific structural variation that underlies IDP function. Here, we perform long-time scale atomistic simulations of 47 representative IDP sequences from the yeast proteome to systematically investigate the relationship between sequence composition and conformational ensemble. To analyze the high-dimensional structural data, we apply uniform manifold approximation and projection (UMAP), a nonlinear dimensionality reduction technique that preserves local structural relationships. The resulting low-dimensional embeddings effectively differentiate IDP ensembles and reveal a novel descriptor─local compactness asymmetry─that quantifies directional differences in chain organization. This metric, denoted
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