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

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

(2020) Erik W. Martin et al.   SCIENCE

Biomolecular Phase Separation: From Molecular Driving Forces to Macroscopic Properties

(2020) Gregory L. Dignon et al.   Annual Review of Physical Chemistry

Liquid–Liquid Phase Separation and Its Mechanistic Role in Pathological Protein Aggregation

(2020) W. Michael Babinchak et al.   JOURNAL OF MOLECULAR BIOLOGY

Hydropathy Patterning Complements Charge Patterning to Describe Conformational Preferences of Disordered Proteins

(2020) Wenwei Zheng et al.   Journal of Physical Chemistry Letters

Liquid network connectivity regulates the stability and composition of biomolecular condensates with many components

(2020) Jorge R. Espinosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measles virus nucleo- and phosphoproteins form liquid-like phase-separated compartments that promote nucleocapsid assembly

(2020) Serafima Guseva et al.   Science Advances

Unraveling Molecular Interactions in Liquid–Liquid Phase Separation of Disordered Proteins by Atomistic Simulations

(2020) Matteo Paloni et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Details of Protein Condensates Probed by Microsecond Long Atomistic Simulations

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

Complete Phase Diagram for Liquid–Liquid Phase Separation of Intrinsically Disordered Proteins

(2019) James McCarty et al.   Journal of Physical Chemistry Letters

Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins

(2019) Upayan Baul et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Spontaneous driving forces give rise to protein−RNA condensates with coexisting phases and complex material properties

(2019) Steven Boeynaems et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Promoting transparency and reproducibility in enhanced molecular simulations

(2019)   NATURE METHODS

LLPSDB: a database of proteins undergoing liquid–liquid phase separation in vitro

(2019) Qian Li et al.   NUCLEIC ACIDS RESEARCH

DisProt: intrinsic protein disorder annotation in 2020

(2019) András Hatos et al.   NUCLEIC ACIDS RESEARCH

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

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

Emerging consensus on the collapse of unfolded and intrinsically disordered proteins in water

(2019) Robert B Best   CURRENT OPINION IN STRUCTURAL BIOLOGY

Collapse Transitions of Proteins and the Interplay Among Backbone, Sidechain, and Solvent Interactions

(2018) Alex S. Holehouse et al.   Annual Review of Biophysics

Inferring properties of disordered chains from FRET transfer efficiencies

(2018) Wenwei Zheng et al.   JOURNAL OF CHEMICAL PHYSICS

An Extended Guinier Analysis for Intrinsically Disordered Proteins

(2018) Wenwei Zheng et al.   JOURNAL OF MOLECULAR BIOLOGY

Why Do Disordered and Structured Proteins Behave Differently in Phase Separation?

(2018) Huan-Xiang Zhou et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

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

Pi-Pi contacts are an overlooked protein feature relevant to phase separation

(2018) Robert McCoy Vernon et al.   eLife

Extreme disorder in an ultrahigh-affinity protein complex

(2018) Alessandro Borgia et al.   NATURE

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

Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water”

(2018) Robert B. Best et al.   SCIENCE

Random-phase-approximation theory for sequence-dependent, biologically functional liquid-liquid phase separation of intrinsically disordered proteins

(2017) Yi-Hsuan Lin et al.   JOURNAL OF MOLECULAR LIQUIDS

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements

(2017) Gustavo Fuertes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water

(2017) Joshua A. Riback et al.   SCIENCE

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

“New Old Pathologies”: AD, PART, and Cerebral Age-Related TDP-43 With Sclerosis (CARTS)

(2016) Peter T. Nelson et al.   JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY

Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment

(2016) Wenwei Zheng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods

(2016) Alessandro Borgia et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Molprobity's ultimate rotamer-library distributions for model validation

(2016) Bradley J. Hintze et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Phase separation of signaling molecules promotes T cell receptor signal transduction

(2016) Xiaolei Su et al.   SCIENCE

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

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

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

Building Force Fields: An Automatic, Systematic, and Reproducible Approach

(2014) Lee-Ping Wang et al.   Journal of Physical Chemistry Letters

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Automated Optimization of Potential Parameters

(2013) Michele Di Pierro et al.   Journal of Chemical Theory and Computation

A Simple Atomic-Level Hydrophobicity Scale Reveals Protein Interfacial Structure

(2013) Lauren H. Kapcha et al.   JOURNAL OF MOLECULAR BIOLOGY

Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy

(2012) H. Hofmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Are Current Molecular Dynamics Force Fields too Helical?

(2008) Robert B. Best et al.   BIOPHYSICAL JOURNAL

Vapor-liquid interfacial properties of fully flexible Lennard-Jones chains

(2008) Felipe J. Blas et al.   JOURNAL OF CHEMICAL PHYSICS

The Role of Solvent Fluctuations in Hydrophobic Assembly†

(2008) Adam P. Willard et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Role of Backbone−Solvent Interactions in Determining Conformational Equilibria of Intrinsically Disordered Proteins

(2008) Hoang T. Tran et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY