mTM-align³

Efficient protein structure comparisons

Find similar structures. Explore their relationships.

Search across structural databases, inspect matching proteins, and align selected structures in one workflow. Beyond structure search, AFDB50 is also clustered: 53,665,797 structures are grouped into 21,057,794 representatives, so a high-speed search scans the representatives and expands every hit to its members. Explore the clusters under Cluster → AFDB50 in the navigation bar.

Structure database search
Multiple structure alignment

Choose databases

1 selected

AFDB50NEW DATABASE53,665,797 proteins
High speed mode only

PDB SCOPe CATH40 BFVD AFDB-SWISSPROT AFDB-HEALTH AFDB-ORGANISM MGNIFY30

Select one or more databases. AFDB50 supports single-chain queries; multimeric queries search PDB only.

Add a query structure

PDB / mmCIF

Try an example

Protein structure in PDB or mmCIF format

Upload structureNo file selected

Or load a structure by ID

Structure source PDB or UniProt ID

Load Protein fills the query; it does not select the search database.

Search settings

High accuracyStructure refinement for other databases High speedEmbedding similarity search

Optional email the results · name this job

Email for results Target name

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Upload compressed File

    Please put all of your structures (2-20 monomeric structures in PDB format) in a folder and compress it.
    Acceptable tarball includes: *.tar, *tar.gz, *.gz, *.tar.bz2、*.bz2、*.xz, *.tar.xz, and *.zip format.
    Download an example zip file

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Other information (optional)

Email: (Optional, where the results will be sent to)

Target name: (Optional, your given name to this target)

References

Lyu, et al, mTM-align2: a server for real-time protein structure database search and alignment, Genomics, Proteomics & Bioinformatics, in press, (2026).

Lyu, et al, Rapid and accurate protein structure database search using inverse folding model and contrastive learning, J Chem Inf Model, 65:13465-13477 (2025). (PDF)