A3DyDB

A3DyDB predicts structure-based aggregation propensities for 6,039 Saccharomyces cerevisiae proteins by applying Aggrescan 3D (A3D) to AlphaFold2 (AF2) structural models to characterize aggregation-prone regions and inform analyses of protein stability and solubility.

Key Features:

• Proteome-wide aggregation predictions: Provides aggregation propensity scores for 6,039 S. cerevisiae proteins derived from AlphaFold2 (AF2) structural models.
• Structure-based aggregation analysis: Uses the Aggrescan 3D (A3D) algorithm to compute intrinsic aggregation propensities from three-dimensional protein structures.
• Mutation impact evaluation: Assesses effects of natural or engineered mutations on predicted protein aggregation, stability, and solubility.
• Proteome-level correlation analyses: Enables investigation of correlations between structural aggregation propensity and other protein properties across the yeast proteome.

Scientific Applications:

• Modeling protein aggregation: Supports structural modeling of aggregation processes relevant to protein misfolding and related disease studies.
• Functional proteomics: Links structure-derived aggregation propensity with protein function and interaction studies in Saccharomyces cerevisiae.
• Genetic engineering and design: Informs design of mutations to modulate protein stability and solubility for experimental and synthetic biology applications.

Methodology:

Aggrescan 3D (A3D) processes AlphaFold2 (AF2) structural models to compute intrinsic aggregation propensities for the included S. cerevisiae proteins.