SoDoPE

SoDoPE predicts protein solubility and identifies soluble domains for recombinant proteins expressed in Escherichia coli by leveraging global structural flexibility quantified with normalized B-factors.

Key Features:

• Global structural flexibility modeling: Uses normalized B-factors to represent global structural flexibility for solubility assessment.
• Solubility-Weighted Index (SWI): Computes an SWI by optimizing B-factor values to provide a quantitative metric of solubility.
• Dataset-derived optimization: Derives optimized B-factors from analysis of a dataset of 12,216 recombinant proteins.
• Region-level soluble domain analysis: Enables analysis and selection of specific protein regions or domains for solubility prediction and optimization.
• Comparative performance: The SWI approach has been demonstrated to outperform many existing solubility prediction methods.
• Integration with TISIGNER suite: Functions as a component within the TISIGNER suite alongside TIsigner and Razor for expression and signal peptide–related analyses.

Scientific Applications:

• Recombinant protein expression in Escherichia coli: Guides selection of soluble domains to improve soluble expression of recombinant proteins in E. coli.
• Yield optimization: Aids strategies to increase the yield of soluble protein for downstream experimental use.
• Structural biology and therapeutic development: Supports production of soluble proteins for structural studies and therapeutic protein development.
• Industrial enzyme production: Informs design choices to enhance solubility of enzymes for industrial applications.

Methodology:

Modeling of global structural flexibility using normalized B-factors, optimization of B-factor values via analysis of 12,216 recombinant proteins, and calculation of the Solubility-Weighted Index (SWI) as the solubility metric.