PhaSePro

PhaSePro curates a database of experimentally validated proteins and systems that undergo liquid-liquid phase separation (LLPS) to support study of membraneless organelle (MO) formation and function.

Key Features:

• Experimentally validated entries: Curated records represent experimentally demonstrated cases of LLPS, focusing on proteins and associated macromolecular systems.
• Biophysical drivers: Integrates information on the biophysical forces driving LLPS, including multivalent weak interactions among proteins and other macromolecules.
• Biological functions and regulatory mechanisms: Annotates biological roles of MOs and regulatory mechanisms, with explicit references to processes such as ribosome biogenesis and RNA degradation.
• LLPS-specific controlled vocabularies: Introduces novel controlled vocabularies specific to LLPS to standardize terminology and data annotation.
• Computational resource support: Provides a curated knowledgebase intended to address gaps in computational resources for identifying LLPS drivers.

Scientific Applications:

• MO formation and dynamics: Enables investigation of formation, composition, and dynamics of membraneless organelles arising from LLPS.
• Identification of LLPS drivers: Supports identification and characterization of proteins and macromolecules that drive LLPS.
• Functional studies: Facilitates study of LLPS-related biological processes, including roles in ribosome biogenesis and RNA degradation.
• Standardized annotation and comparison: Allows standardized annotation and cross-study comparison using LLPS-specific controlled vocabularies.
• Computational method development: Serves as a curated dataset for developing and benchmarking computational predictors of LLPS drivers.

Methodology:

Manual curation of experimentally validated LLPS cases and integration of information on biophysical forces, biological functions, regulatory mechanisms, and LLPS-specific controlled vocabularies.