Fix ipSAE: add 15A distance filter, PAE cutoff 10, max of asymmetric scores

Fix ipSAE: correct name, use max of asymmetric scores, PAE cutoff 10

Update lis.py and add seq_extract.py

Add lis.py CLI tool and update README

Add LIVIA web tool references to Usage section

Fix formatting: restore AF2 mention, add blank line between sections

Remove LIVIA references

Update LIVIA references (renamed from in_silico_ppi_analysis)

Update web tool links to in_silico_ppi_analysis

Add AlphaFold3-ChimeraX web tool to Usage section

Add ChimeraX visualization tools, update FlyPredictome to >1.7M predictions, add Claude Code to AI declaration

Update README.md

Add files via upload

Created using Colab

Created using Colab