Skip to content

ipSAE Scoring

Overview

ipSAE (Interface Protein Structure Analysis and Evaluation) provides quantitative metrics for evaluating protein-protein interactions in designed complexes. This optional analysis complements PRODIGY predictions with detailed structural assessments.

What is ipSAE?

ipSAE analyzes the geometric and chemical properties of protein interfaces to score interaction quality, helping identify the most promising designed binders.

Enabling ipSAE

Add the --run_ipsae flag to your pipeline command:

nextflow run seqeralabs/nf-proteindesign \
    -profile docker \
    --input samplesheet.csv \
    --run_ipsae \
    --outdir results

Output Files

ipSAE generates detailed scoring files for each design:

results/
└── {sample}/
    └── ipsae/
        ├── design_1_ipsae_scores.csv
        ├── design_2_ipsae_scores.csv
        └── ...

Score Metrics

Each file contains multiple interaction quality metrics:

Metric Description Better Value
Interface Area Contact surface area Larger
Shape Complementarity Geometric fit Higher (0-1)
Contact Density Residues per area Higher
Hydrogen Bonds H-bond count More
Salt Bridges Ionic interactions More
Hydrophobic Contacts Apolar interactions Balanced

Comparing ipSAE and PRODIGY

Feature ipSAE PRODIGY
Focus Interface quality Binding affinity
Output Multiple metrics ΔG and Kd
Speed Fast Fast
Best For Structural analysis Affinity ranking

Use Both

Combine ipSAE and PRODIGY for comprehensive evaluation: 

nextflow run ... --run_ipsae --run_prodigy

Interpreting Results

Example Output

design_id,interface_area,shape_comp,contact_density,h_bonds,salt_bridges,hydrophobic
design_1,1543.2,0.68,0.045,12,3,28
design_2,1289.7,0.72,0.052,15,4,22
design_3,1678.9,0.61,0.038,9,2,31

Quality Thresholds

Good Interfaces

  • Interface Area: > 1200 Ų
  • Shape Complementarity: > 0.65
  • H-bonds: > 10
  • Salt Bridges: ≥ 2

Next Steps

Coming Soon

Detailed ipSAE analysis guide with visualization examples.