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Prediction of Liquid-Liquid Phase Separation Proteins Using Machine Learning

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Phase separation, pore structure, and properties of nanofibrous gelatin scaffolds

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Nuclear bodies: the emerging biophysics of nucleoplasmic phases

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

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A Phase Separation Model for Transcriptional Control

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

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Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates

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A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression

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Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles

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Properties of Stress Granule and P-Body Proteomes

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Liquid–liquid phase separation in cellular signaling systems

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ALS Mutations Disrupt Phase Separation Mediated by α-Helical Structure in the TDP-43 Low-Complexity C-Terminal Domain

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Liquid–liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau

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Three archetypical classes of macromolecular regulators of protein liquid–liquid phase separation

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

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DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists

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

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MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins

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RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

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HMMER web server: 2018 update

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DrLLPS: a data resource of liquid–liquid phase separation in eukaryotes

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

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PhaSepDB: a database of liquid–liquid phase separation related proteins

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PhaSePro: the database of proteins driving liquid–liquid phase separation

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

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Prevalence and functionality of intrinsic disorder in human FG-nucleoporins

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Liquid-liquid phase separation of the intrinsically disordered AB region of hRXRγ is driven by hydrophobic interactions

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A protein pre-trained model-based approach for the identification of the liquid-liquid phase separation (LLPS) proteins

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

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A variational graph-partitioning approach to modeling protein liquid-liquid phase separation

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GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein

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JMJD3 intrinsically disordered region links the 3D-genome structure to TGFβ-dependent transcription activation

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PICNIC accurately predicts condensate-forming proteins regardless of their structural disorder across organisms

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Proteomic analysis of heat-stable proteins revealed an increased proportion of proteins with compositionally biased regions

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

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In silico prediction of in vitro protein liquid–liquid phase separation experiments outcomes with multi-head neural attention

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LLPSDB v2.0: an updated database of proteins undergoing liquid–liquid phase separation in vitro

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PlantGSAD: a comprehensive gene set annotation database for plant species

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Cingulin unfolds ZO-1 and organizes myosin-2B and γ-actin to mechanoregulate apical and tight junction membranes

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

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Machine learning models for predicting protein condensate formation from sequence determinants and embeddings

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Identification of Phase Separating Proteins With Distributed Reduced Alphabet Representations of Sequences

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Tudor staphylococcal nuclease is a docking platform for stress granule components and is essential for SnRK1 activation in Arabidopsis

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Phase separation in synthetic biology

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Protein Databases Related to Liquid–Liquid Phase Separation

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Studying Peptide-Metal Ion Complex Structures by Solution-State NMR

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Evidence That the Adenovirus Single-Stranded DNA Binding Protein Mediates the Assembly of Biomolecular Condensates to Form Viral Replication Compartments

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