ProteinUbiquitinationEngine

Ubiquitin-Proteasome System Analysis Pipeline

A pure-Python pipeline for ubiquitination site prediction, E3 ligase network analysis, and proteasomal degradation kinetics.

Features

• Ubiquitination site prediction (K residue sequence context, PWM scoring)
• E3 ligase substrate network (RING/HECT/RBR classification)
• Ubiquitin chain type scoring (K48/K63/K11 linkage specificity)
• Proteasomal degradation kinetics ODE
• Ubiquitin code decoding (chain type → cellular outcome)

Results

• 500 proteins × ubiquitination sites, 100 E3 ligases
• K residues scored: 7339, True sites: 1281
• Site prediction AUC: 0.825
• E3 distribution: RING=65%, HECT=24%, RBR=11%
• Dominant outcome: Degradation (K48-linked)

Usage

pip install numpy scipy matplotlib
python protein_ubiquitination_engine.py

Tags

ubiquitination proteasome e3-ligase protein-degradation ubiquitin-code post-translational-modification