Intrinsically disordered regions that drive phase separation form a robustly distinct protein class

Prediction of liquid–liquid phase separating proteins using machine learning

(2022) Xiaoquan Chu et al.   BMC BIOINFORMATICS

Phase separation driven by interchangeable properties in the intrinsically disordered regions of protein paralogs

(2022) Shih-Hui Chiu et al.   Communications Biology

An Interpretable Machine-Learning Algorithm to Predict Disordered Protein Phase Separation Based on Biophysical Interactions

(2022) Hao Cai et al.   Biomolecules

Phase separation of DNA: from past to present

(2021) John T. King et al.   BIOPHYSICAL JOURNAL

Computational Screening of Biological Phase-separating Proteins

(2021) Boyan Shen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Integration of Data from Liquid–Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers

(2021) Nazanin Farahi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2021) Thomas Dannenhoffer-Lafage et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Learning the molecular grammar of protein condensates from sequence determinants and embeddings

(2021) Kadi L. Saar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metapredict: a fast, accurate, and easy-to-use predictor of consensus disorder and structure

(2021) Ryan J. Emenecker et al.   BIOPHYSICAL JOURNAL

Beta turn propensity and a model polymer scaling exponent identify intrinsically disordered phase-separating proteins

(2021) Elisia A. Paiz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Understanding How Coacervates Drive Reversible Small Molecule Reactions to Promote Molecular Complexity

(2021) Michael I. Jacobs et al.   LANGMUIR

Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains

(2021) Anne Bremer et al.   Nature Chemistry

Molecular interactions contributing to FUS SYGQ LC-RGG phase separation and co-partitioning with RNA polymerase II heptads

(2021) Anastasia C. Murthy et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2021) Giulio Tesei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PANTHER : Making genome‐scale phylogenetics accessible to all

(2021) Paul D. Thomas et al.   PROTEIN SCIENCE

What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?

(2021) Julie D. Forman-Kay et al.   RNA

RNA Droplets

(2020) Kevin Rhine et al.   Annual Review of Biophysics

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

(2020) Erik W. Martin et al.   SCIENCE

Protein stability governed by its structural plasticity is inferred by physicochemical factors and salt bridges

(2020) Anindya S. Panja et al.   Scientific Reports

Identifying sequence perturbations to an intrinsically disordered protein that determine its phase-separation behavior

(2020) Benjamin S. Schuster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Connecting Coil-to-Globule Transitions to Full Phase Diagrams for Intrinsically Disordered Proteins

(2020) Xiangze Zeng et al.   BIOPHYSICAL JOURNAL

Sequence-Based Prediction of Metamorphic Behavior in Proteins

(2020) Nanhao Chen et al.   BIOPHYSICAL JOURNAL

Enzymatic Reactions inside Biological Condensates

(2020) Yi Zhang et al.   JOURNAL OF MOLECULAR BIOLOGY

Phase separation by ssDNA binding protein controlled via protein−protein and protein−DNA interactions

(2020) Gábor M. Harami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phase Separation as a Missing Mechanism for Interpretation of Disease Mutations

(2020) Brian Tsang et al.   CELL

Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations

(2020) Wenwei Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computational resources for identifying and describing proteins driving liquid–liquid phase separation

(2020) Rita Pancsa et al.   BRIEFINGS IN BIOINFORMATICS

Molecular Mechanisms of TDP-43 Misfolding and Pathology in Amyotrophic Lateral Sclerosis

(2019) Archana Prasad et al.   Frontiers in Molecular Neuroscience

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)

(2019) Huaiyu Mi et al.   Nature Protocols

Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates

(2019) Gabriele Orlando et al.   BIOINFORMATICS

Single Amino Acid Substitutions in Stickers, but Not Spacers, Substantially Alter UBQLN2 Phase Transitions and Dense Phase Material Properties

(2019) Yiran Yang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Temperature-Controlled Liquid–Liquid Phase Separation of Disordered Proteins

(2019) Gregory L. Dignon et al.   ACS Central Science

Molecular interactions underlying liquid−liquid phase separation of the FUS low-complexity domain

(2019) Anastasia C. Murthy et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Liquid–Liquid Phase Separation in Disease

(2019) Simon Alberti et al.   Annual Review of Genetics

First-generation predictors of biological protein phase separation

(2019) Robert M Vernon et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Impact of Heat on Coil Hydrodynamic Size Yields the Energetics of Denatured State Conformational Bias

(2019) Lance R. English et al.   JOURNAL OF PHYSICAL CHEMISTRY B

LASSI: A lattice model for simulating phase transitions of multivalent proteins

(2019) Jeong-Mo Choi et al.   PLoS Computational Biology

Function and Regulation of Phase-Separated Biological Condensates

(2018) Xiao-Han Li et al.   BIOCHEMISTRY

Modeling the Early Stages of Phase Separation in Disordered Elastin-like Proteins

(2018) Yue Zhang et al.   BIOPHYSICAL JOURNAL

A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins

(2018) Jie Wang et al.   CELL

Ubiquitin Modulates Liquid-Liquid Phase Separation of UBQLN2 via Disruption of Multivalent Interactions

(2018) Thuy P. Dao et al.   MOLECULAR CELL

Phase separation of a yeast prion protein promotes cellular fitness

(2018) Titus M. Franzmann et al.   SCIENCE

Sequence determinants of protein phase behavior from a coarse-grained model

(2018) Gregory L. Dignon et al.   PLoS Computational Biology

The molecular language of membraneless organelles

(2018) Edward Gomes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments

(2018) Jill J. Bouchard et al.   MOLECULAR CELL

Relation between single-molecule properties and phase behavior of intrinsically disordered proteins

(2018) Gregory L. Dignon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SCOPe: classification of large macromolecular structures in the structural classification of proteins—extended database

(2018) John-Marc Chandonia et al.   NUCLEIC ACIDS RESEARCH

Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation

(2017) Jacob P. Brady et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsic α helix propensities compact hydrodynamic radii in intrinsically disordered proteins

(2017) Lance R. English et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

Phase separation and mechanical properties of an elastomeric biomaterial from spider wrapping silk and elastin block copolymers

(2016) Lisa D. Muiznieks et al.   BIOPOLYMERS

Phase separation in biology; functional organization of a higher order

(2016) Diana M. Mitrea et al.   Cell Communication and Signaling

Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein

(2016) Chi W. Pak et al.   MOLECULAR CELL

DisProt 7.0: a major update of the database of disordered proteins

(2016) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

Phase separation of signaling molecules promotes T cell receptor signal transduction

(2016) Xiaolei Su et al.   SCIENCE

Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities

(2016) Maria E. Tomasso et al.   PLoS Computational Biology

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

(2015) Yuan Lin et al.   MOLECULAR CELL

The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics

(2015) Shana Elbaum-Garfinkle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spider wrapping silk fibre architecture arising from its modular soluble protein precursor

(2015) Marie-Laurence Tremblay et al.   Scientific Reports

PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition

(2014) A. K. Lancaster et al.   BIOINFORMATICS

The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities

(2014) Petr Klus et al.   BIOINFORMATICS

Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates

(2014) Vladimir N. Uversky et al.   FEBS LETTERS

Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins

(2014) Romel B. Perez et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures

(2013) Naomi K. Fox et al.   NUCLEIC ACIDS RESEARCH

Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites

(2013) W. Austin Elam et al.   PROTEIN SCIENCE

Temperature effects on the hydrodynamic radius of the intrinsically disordered N-terminal region of the p53 protein

(2013) Timothy D. Langridge et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins

(2012) Lukasz P Kozlowski et al.   BMC BIOINFORMATICS

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

A Systematic Survey Identifies Prions and Illuminates Sequence Features of Prionogenic Proteins

(2009) Simon Alberti et al.   CELL

Germline P Granules Are Liquid Droplets That Localize by Controlled Dissolution/Condensation

(2009) C. P. Brangwynne et al.   SCIENCE

Denatured-State Energy Landscapes of a Protein Structural Database Reveal the Energetic Determinants of a Framework Model for Folding

(2008) Suwei Wang et al.   JOURNAL OF MOLECULAR BIOLOGY

SEQATOMS: a web tool for identifying missing regions in PDB in sequence context

(2008) B. W. Brandt et al.   NUCLEIC ACIDS RESEARCH

TOP-IDP-Scale: A New Amino Acid Scale Measuring Propensity for Intrinsic Disorder

(2008) Andrew Campen et al.   PROTEIN AND PEPTIDE LETTERS