LIVIA — FlyPredictome Analysis

Interaction Analysis Summary

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Click a row to switch ranks. This updates all visualizations and the script below.

Rank	Symbol 1	Symbol 2	iLIS	iLIA	iLISA	ipTM	LIR (A/B)	cLIR (A/B)	Len (A/B)

iLIS: ≥0.551 (1% FDR) ≥0.339 (5% FDR) ≥0.223 (10% FDR) <0.223 (below threshold)

iLIS (average): ≥0.303 (1% FDR) ≥0.120 (5% FDR) ≥0.073 (10% FDR) <0.073 (below threshold)

Thresholds based on large-scale Y2H reference sets in yeast, fly, and human predicted using ColabFold. See Kim et al. 2025 for iLIS benchmark details. Rank 1 (determined by ipTM) may not have the highest iLIS.

Reported Interactions (MIST)

Predicted Aligned Error (PAE)

PAE matrix showing prediction confidence between all residue pairs. Blue = low error (high confidence).

Sequence Viewer

Light background = LIR (PAE ≤ 12 Å). Dark background = cLIR (PAE ≤ 12 Å & Cβ ≤ 8 Å). Each chain uses its own color.

Linear Contact Map

Lines connect cLIR residue pairs within Cβ distance in the 3D structure. Per-rank structures fetched automatically.

Circular Contact Map

Arcs represent chains (proportional to length). Lines connect cLIR residue pairs in physical contact.

Selected Rank

3D Structure Viewer

Interactive 3D preview powered by Mol* (Sehnal et al. 2021). LIR regions shown as cartoons; cLIR residues highlighted. Drag to rotate, scroll to zoom.

Visualization Script

Options LIR Display Options

Fill gaps ≤ residues | Min segment ≥ residues

Gap filling bridges short breaks for continuous cartoon. Min segment removes isolated LIR fragments shorter than the threshold.

Show complete structure (display all residues instead of LIR only) Gray non-LIR (color non-interacting residues gray) Color Scheme

Chain A (Protein 1)

LIR — confident domain (PAE ≤ 12)

#80CBC4

cLIR — confident interface (PAE ≤ 12 & Cβ ≤ 8 Å)

#00897B

Chain B (Protein 2)

LIR — confident domain (PAE ≤ 12)

#FFAB91

cLIR — confident interface (PAE ≤ 12 & Cβ ≤ 8 Å)

#E64A19

Presets — gradient (LIR light, cLIR dark)

Teal / Coral

Blue / Orange

Purple / Gold

Slate / Rose

Indigo / Tangerine

Green / Red

Presets — high contrast (all 4 colors distinct)

Cyan / Navy / Peach / Crimson

Sky / Indigo / Salmon / Red

Lime / Forest / Gold / Maroon

Mint / DarkTeal / Apricot / Burnt

Orchid / Purple / Yellow / Fire

Blue / Navy / Sage / Ember

Presets — solid

Teal / Coral

Blue / Orange

Purple / Gold

Slate / Rose

Steel / Wheat

Cornflower / Tomato

SkyBlue / Gold

LightGreen / Plum

Salmon / Teal

Presets — coloring modes

pLDDT

bychain

bypolymer

Show complete structure Gray non-LIR

↓ Download .cxc ↓ Download .pdb

The .pdb link opens the file from FlyPredictome. Save it in the same folder as the script file, then open the script in ChimeraX or PyMOL.

How to Use (Full guide)

Quick Start

Go to FlyPredictome and search for a protein pair
Copy the FlyPredictome result page URL
Paste the URL above and click Generate
Download the script (.cxc or .pml) and structure file, place both in the same folder
Open the script in ChimeraX (.cxc) or PyMOL (.pml)

AFM-LIS Metrics (Kim et al. 2024, 2025)

iLIS	integrated LIS — √(LIS × cLIS)
iLIA	integrated LIA — √(LIA × cLIA), geometric mean of interface area counts
iLISA	integrated LISA — iLIS × iLIA, overall binding strength
LIS	Local Interaction Score — normalized PAE confidence (0–1)
cLIS	contact-filtered LIS — restricted to direct contacts
LIR	Local Interaction Residues (PAE ≤ 12 Å)
cLIR	contact-filtered LIR (PAE ≤ 12 Å & Cβ ≤ 8 Å)

Confidence Metric (from ColabFold)

ipTM

interface predicted TM-score — global interface confidence from the prediction model

PAE (Predicted Aligned Error) measures how confidently the model predicts the relative position of two residues — lower values indicate higher confidence.

References

Kim et al. 2024 — Enhanced PPI Discovery via AlphaFold-Multimer
Kim et al. 2025 — A Structure-Guided Kinase–Transcription Factor Interactome Atlas