LIVIA — AlphaFold DB Monomer Subdomain Analysis

Subdomain Interaction Map

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

Sequence Viewer

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

Region & Domain Map

Auto-detected regions vs UniProt domains and TED domains (AlphaFold DB). Aligned to residue position.

Region Pair Summary

Region Pair	iLIS	iLIA	iLISA	LIS	cLIS	LIR (i/j)	cLIR (i/j)

↓ Download CSV

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 selected regions only) Gray non-LIR (color non-interacting residues gray) Cutoffs

PAE cutoff (Å):

Cβ cutoff (Å):

Color Scheme

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

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

How to Use (Full guide)

Quick Start

Enter a UniProt ID (e.g., P28482) and click Fetch
Define two or more regions of interest by residue range
Click Calculate to compute interaction metrics
Review the PAE map, iLIS scores, and region pair table
Download the script and .pdb file, place them 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)

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 — Monomer and dimer predictions

LIVIA — AlphaFold DB Monomer Subdomain Analysis alpha