LIVIA — AlphaFold DB Dimer Analysis

Interaction Analysis Summary

Protein A	Protein B	iLIS	iLIA	iLISA	ipSAE	ipTM	LIS	cLIS	LIR (A/B)	cLIR (A/B)

↓ Download CSV

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

Maps

Sequence Viewer

Light background = LIR (PAE ≤ 12 Å). Dark background with white text = 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. Color gradient from chain A to chain B. UniProt domain annotations shown when available.

Circular Contact Map

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

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) Cutoffs

PAE cutoff (Å):

Cβ cutoff (Å):

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

Color Scheme

Chain A

LIR

#80CBC4

cLIR

#00897B

Chain B

LIR

#FFAB91

cLIR

#E64A19

Show complete structure Gray non-LIR

↓ Download .cxc ↓ Download .cif

Place the script and .cif files in the same folder, then open the script in ChimeraX or PyMOL.

How to Use (Full guide)

Quick Start

Enter a UniProt ID and click Search Dimers
Select a dimer from the results table
Explore PAE, LIS, and cLIS maps
Review metrics (iLIS, LIS, cLIS, ipTM, pDockQ2, pLDDT) and maps
Download the script and .cif file, place in the same folder, then 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 Metrics (from AlphaFold DB)

ipTM	interface predicted TM-score — global interface confidence from the prediction model
ipSAE	interaction prediction Score from Aligned Errors (Dunbrack, 2025)

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
AlphaFold Protein Structure Database — Dimer predictions