ArticleJournal of chemical theory and computation2020
Maximum Entropy Optimized Force Field for Intrinsically Disordered Proteins.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- Article
- Valency-Limited Molecular Dynamics Simulations of Stickers-and-Spacers Polymers Reveal a Tradeoff Between Condensation and Organization.bioRxiv : the preprint server for biology · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.Journal of chemical theory and computation · 2026Article
- MOFF2: A Transferable Coarse-Grained Protein Force Field for Predictive Condensate Simulations.bioRxiv : the preprint server for biology · 2026Article
- Advances and challenges in multiscale biomolecular simulations: artificial intelligence-driven paradigm shift.Quantitative biology (Beijing, China) · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.Journal of chemical theory and computation · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.ArXiv · 2026Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.bioRxiv : the preprint server for biology · 2025Article
- Protein language model identifies disordered, conserved motifs implicated in phase separation.eLife · 2025Article
- Combining simulations and experiments - a perspective on maximum entropy methods.Physical chemistry chemical physics : PCCP · 2025Review
- Conformational dynamics and multimodal interaction of Paxillin with the focal adhesion targeting domain.Science advances · 2025Article
- Conformational dynamics and multi-modal interaction of Paxillin with the Focal Adhesion Targeting Domain.bioRxiv : the preprint server for biology · 2025Article
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins.Protein science : a publication of the Protein Society · 2025Article
- Microphase separation produces interfacial environment within diblock biomolecular condensates.eLife · 2025Article
- Energy landscape analysis of the development of the chromosome structure across the cell cycle.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- Nonspecific Yet Selective Interactions Contribute to Small Molecule Condensate Binding.Journal of chemical theory and computation · 2024Article
- Article
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2 authors.
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Abstract
Intrinsically disordered proteins (IDPs) constitute a significant fraction of eukaryotic proteomes. High-resolution characterization of IDP conformational ensembles can help elucidate their roles in a wide range of biological processes but remains challenging both experimentally and computationally. Here, we present a generic algorithm to improve the accuracy of coarse-grained IDP models using a diverse set of experimental measurements. It combines maximum entropy optimization and least-squares regression to systematically adjust model parameters and improve the agreement between simulation and experiment. We successfully applied the algorithm to derive a transferable force field, which we term the maximum entropy optimized force field (MOFF), for de novo prediction of IDP structures. Statistical analysis of force field parameters reveals features of amino acid interactions not captured by potentials designed to work well for folded proteins. We anticipate its combination of efficiency and accuracy will make MOFF useful for studying the phase separation of IDPs, which drives the formation of various biological compartments.
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