LIVIA — AlphaFold DB Dimer Analysis

🔖 Browsing an AlphaFold DB entry? Jump straight to this analysis with the LIVIA bookmarklet — one click, no copy-paste. Get it →

Fetch Dimer Prediction (the prediction is fetched from AlphaFold DB; all analysis runs in your browser · what LIVIA looks up online)

UniProt ID, AlphaFold Model ID, or AlphaFold DB URL

Heterodimer: Homodimer:

Not all proteins have dimer predictions. Browse AlphaFold DB to find available complexes, then paste the URL or model ID here.

Interaction Analysis Summary

Show iLIA/LIR/cLIR columns

Protein A	Protein B	iLIS	iLISA	ipSAE	actifpTM	ipTM	LIS	cLIS	pDockQ	LIpDockQ	pDockQ2	LIpDockQ2	iLIA	LIR (A/B)	cLIR (A/B)

↓ Download CSV

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

Thresholds based on large-scale Y2H reference sets in yeast, fly, and human predicted using ColabFold. See Kim et al., 2026, for iLIS benchmark details.

Label Settings

Names show on left top Style chip color font Length show format color font Domains show order color Custom

Maps

Dimer vs Monomer Comparison (Intra-chain LIS & pLDDT)

Compares per-residue metrics when the chain is predicted alone (monomer) vs. as part of a complex (dimer). Intra-chain LIS measures internal folding confidence within the same chain. Green shading = gain in dimer context; red = loss.

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.

domains: UniProt/Pfam TED pLDDT chain IDs swap chains (top↔bottom) x-ticks

Circular Contact Map

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

labels chain IDs length ticks pLDDT domains: UniProt/Pfam TED label direction

Reported Interactions (MIST, BioGRID)

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. If the viewer appears empty, refresh the page.

Visualization Script

Local Interaction Residue (LIR) Display

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

↓ Full structure .cif ↓ .cxc · for full

The whole complex. Surfaces include the floppy N/C-terminal tails.

↓ Partial structure .cif ↓ .cxc · for partial

Every subunit kept; each interface chain trimmed to exactly the LIR segments shown (Fill gaps / Min segment honored). Residue numbers preserved.

Each script opens its matching structure file (distinct names, so nothing overwrites). Download a script + its structure into the same folder, then open the script in ChimeraX (.cxc) or PyMOL (.pml).

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; Kim et al. 2026)

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)

Other interface scores

ipTM	interface predicted TM-score — global interface confidence from the prediction model
ipSAE	interaction prediction Score from Aligned Errors (Dunbrack, 2025)
actifpTM	actual interface pTM (Varga et al., 2025)

pDockQ family

pDockQ	predicted DockQ from the mean pLDDT of the interface and the number of contacting residue pairs (Cβ ≤ 8 Å), with no PAE (Bryant et al., 2022)
pDockQ2	pDockQ with each contact weighted by its PAE, per chain (Zhu et al., 2023)
LIpDockQ	the pDockQ formula computed only on cLIR pairs (PAE ≤ 12 Å and Cβ ≤ 8 Å), so contacts the PAE does not support no longer count (Kim & Perrimon, 2026)
LIpDockQ2	the pDockQ2 formula on cLIR pairs only, so a small confident interface is not diluted by a large, poorly placed contact surface (Kim & Perrimon, 2026)

Because their constants were fitted to DockQ on the original interfaces, LIpDockQ and LIpDockQ2 rank predictions; they are not DockQ estimates.

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