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A Data-Driven Hydrophobicity Scale for Predicting Liquid–Liquid Phase Separation of Proteins

https://doi.org/10.1021/acs.jpcb.0c11479

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What this work says

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Thermodynamic origins of two-component multiphase condensates of proteins

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Deciphering the liquid–liquid phase separation induced modulation in the structure, dynamics, and enzymatic activity of an ordered protein β-lactoglobulin

inferred← citeshttps://doi.org/10.1039/d3sm00633fopenalex-snapshot

Multi-scale molecular simulation of random peptide phase separation and its extended-to-compact structure transition driven by hydrophobic interactions

inferred← citeshttps://doi.org/10.1039/d4me00197dopenalex-snapshot

Toward understanding biomolecular materials comprising intrinsically disordered proteins via simulation and experiment

inferred← citeshttps://doi.org/10.1042/bst20230618openalex-snapshot

Backbone interactions and secondary structures in phase separation of disordered proteins

inferred← citeshttps://doi.org/10.1063/5.0062687openalex-snapshot

Salt dependent phase behavior of intrinsically disordered proteins from a coarse-grained model with explicit water and ions

inferred← citeshttps://doi.org/10.1063/5.0131028openalex-snapshot

Phase diagrams—Why they matter and how to predict them

inferred← citeshttps://doi.org/10.1063/5.0176306openalex-snapshot

Fine structures of intrinsically disordered proteins

inferred← citeshttps://doi.org/10.1063/5.0253522openalex-snapshot

Intrinsic hydrophobicity of IDP-based biomolecular condensates drives their partial drying on membrane surfaces

inferred← citeshttps://doi.org/10.1063/5.0275549openalex-snapshot

Anomalous thermoresponsive phase behavior in a minimal lattice model mimicking proteins

inferred← citeshttps://doi.org/10.1063/5.0307183openalex-snapshot

In search of shape in the unshaped: Constructing ensembles of intrinsically disordered proteins

inferred← citeshttps://doi.org/10.1063/5.0346259openalex-snapshot

Liquid–liquid phase separation in a minimal explicit-solvent lattice model mimicking protein solutions

inferred← citeshttps://doi.org/10.1073/pnas.2111696118openalex-snapshot

Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties

inferred← citeshttps://doi.org/10.1073/pnas.2417920122openalex-snapshot

Prediction of phase-separation propensities of disordered proteins from sequence

inferred← citeshttps://doi.org/10.1073/pnas.2425422122openalex-snapshot

Amino acid transfer free energies reveal thermodynamic driving forces in biomolecular condensate formation

inferred← citeshttps://doi.org/10.1073/pnas.2531932123openalex-snapshot

amyloid-predict and LLPS-predict: Predicting phase separation propensities in the intrinsically disordered proteome

inferred← citeshttps://doi.org/10.1080/00268976.2024.2425757openalex-snapshot

Capturing single-molecule properties does not ensure accurate prediction of biomolecular phase diagrams

inferred← citeshttps://doi.org/10.1080/23746149.2025.2592547openalex-snapshot

Modeling biomolecular condensates across scales: atomistic, coarse-grained, and data-driven approaches

inferred← citeshttps://doi.org/10.1101/2020.07.06.189613openalex-snapshot

Beta turn propensity and a model polymer scaling exponent identify disordered proteins that phase separate

inferred← citeshttps://doi.org/10.1101/2021.09.08.459482openalex-snapshot

Charged sequence motifs increase affinity towards liquid-liquid phase separation

inferred← citeshttps://doi.org/10.1101/2022.04.19.488761openalex-snapshot

The stoichiometric interaction model for mesoscopic molecular dynamics simulations of liquid-liquid phase separation

inferred← citeshttps://doi.org/10.1101/2024.06.14.599027openalex-snapshot

Heterogenous organization in condensates of multiple transcription factors in embryonic stem cells

inferred← citeshttps://doi.org/10.1101/2024.11.02.621395openalex-snapshot

CELF2 promotes tau exon 10 inclusion via hinge domain-mediated nuclear condensation

inferred← citeshttps://doi.org/10.1101/2025.08.06.668966openalex-snapshot

Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins

inferred← citeshttps://doi.org/10.1101/2025.11.24.690320openalex-snapshot

Slab-PTM: A Coarse-Grained Force-Field Parameter Patch for Modeling Post-Translational Modification Effects on Biomolecular Condensates

inferred← citeshttps://doi.org/10.1126/sciadv.adm9926openalex-snapshot

Design of intrinsically disordered protein variants with diverse structural properties

inferred← citeshttps://doi.org/10.1146/annurev-physchem-082423-032133openalex-snapshot

Computational Modeling of Biomolecular Phase Separation: Current Progress and Open Challenges

inferred← citeshttps://doi.org/10.1186/s40543-026-00564-xopenalex-snapshot

MetaRT: structure-embedded stacked ensemble machine learning prediction of retention time of short peptides

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1009578openalex-snapshot

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1011321openalex-snapshot

Micelle-like clusters in phase-separated Nanog condensates: A molecular simulation study

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1011442openalex-snapshot

OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1012737openalex-snapshot

Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates

inferred← citeshttps://doi.org/10.2139/ssrn.5437999openalex-snapshot

Multivalency in Tau–Microtubule interactions: Heterogeneous association and functional implications

inferred← citeshttps://doi.org/10.26434/chemrxiv-2024-4z37hopenalex-snapshot

Recent progress in modeling and simulation ofbiomolecular crowding and condensation insidecells

inferred← citeshttps://doi.org/10.32388/d09yndopenalex-snapshot

Melatonin, ATP, and Cataracts: The Two Faces of Crystallin Phase Separation

inferred← citeshttps://doi.org/10.3390/biom13030530openalex-snapshot

Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery

inferred← citeshttps://doi.org/10.3390/biom13040625openalex-snapshot

Effects of Mass Change on Liquid–Liquid Phase Separation of the RNA-Binding Protein Fused in Sarcoma

inferred← citeshttps://doi.org/10.3390/molecules27175726openalex-snapshot

Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions

inferred← citeshttps://doi.org/10.3390/ph18111711openalex-snapshot

Protein Representation in Metric Spaces for Protein Druggability Prediction: A Case Study on Aspirin

inferred← citeshttps://doi.org/10.52601/bpr.2022.210029openalex-snapshot

Theoretical modelling of liquid–liquid phase separation: from particle-based to field-based simulation

inferred← citeshttps://doi.org/10.64898/2026.02.03.703500openalex-snapshot

On the Use of Double Mutant Cycles to Probe the Molecular Interactions in Biomolecular Condensates

inferred← citeshttps://doi.org/10.64898/2026.08.02.742325openalex-snapshot

Valency-Limited Molecular Dynamics Simulations of Stickers-and-Spacers Polymers Reveal a Tradeoff Between Condensation and Organization

inferred← citeshttps://doi.org/10.7554/elife.100284openalex-snapshot

Electrostatics of salt-dependent reentrant phase behaviors highlights diverse roles of ATP in biomolecular condensates

inferred← citeshttps://doi.org/10.7554/elife.100284.1openalex-snapshot

Electrostatics of Salt-Dependent Reentrant Phase Behaviors Highlights Diverse Roles of ATP in Biomolecular Condensates

inferred← citeshttps://doi.org/10.7554/elife.100284.2openalex-snapshot

Electrostatics of Salt-Dependent Reentrant Phase Behaviors Highlights Diverse Roles of ATP in Biomolecular Condensates

inferred← citeshttps://doi.org/10.7554/elife.100284.3openalex-snapshot

Electrostatics of salt-dependent reentrant phase behaviors highlights diverse roles of ATP in biomolecular condensates

inferred← citeshttps://doi.org/10.7554/elife.111124openalex-snapshot

Role of desolvation on biomolecular liquid–liquid phase separation

inferred← citeshttps://doi.org/10.7554/elife.111124.1openalex-snapshot

Role of desolvation on biomolecular liquid-liquid phase separation

inferred← citeshttps://doi.org/10.7554/elife.111124.2openalex-snapshot

Role of desolvation on biomolecular liquid-liquid phase separation

inferred← citeshttps://doi.org/10.7554/elife.111124.3openalex-snapshot

Role of desolvation on biomolecular liquid–liquid phase separation

inferred← citeshttps://doi.org/10.7554/elife.90750openalex-snapshot

Microphase separation produces interfacial environment within diblock biomolecular condensates

inferred← citeshttps://doi.org/10.7554/elife.90750.1openalex-snapshot

Frustrated Microphase Separation Produces Interfacial Environment within Biological Condensates

inferred← citeshttps://doi.org/10.7554/elife.90750.2openalex-snapshot

Microphase Separation Produces Interfacial Environment within Diblock Biomolecular Condensates

inferred← citeshttps://doi.org/10.7554/elife.90750.3openalex-snapshot

Microphase Separation Produces Interfacial Environment within Diblock Biomolecular Condensates

inferred← citeshttps://doi.org/10.7554/elife.90750.4openalex-snapshot

Microphase separation produces interfacial environment within diblock biomolecular condensates

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