AlphaFind v2

AlphaFind v2 is a tool for fast, structure‑based search for protein structures against the AlphaFold DB (https://alphafold.ebi.ac.uk/) and TED DB (https://ted.cathdb.info/). The tool uses protein‑level embeddings to provide a rapid pre‑filter, with top candidates undergoing TM-Score, RMSD and residue‑level alignments computations. Four complementary search modes are available: (i) whole‑chain search, (ii) pLDDT‑aware search that restricts similarity to high‑confidence regions, (iii) domain search against the TED database, and (iv) multidomain search that combines several chain‑level matches into a single score. Users can restrict queries to a given organism, CATH superfamily or to proteins with experimental structures, and submit queries by UniProt/AlphaFold identifier. Results comprise a ranked list with similarity metrics, rich metadata and an interactive 3‑D superposition view. The service is freely accessible at https://alphafind.ics.muni.cz/.