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GTalign web server

High-performance search and alignment for macromolecular (protein, RNA, DNA) structures and complexes.

This server is free and open to all users and there is no login requirement.

Paste structure: (?)

Enter your structures in PDB and/or mmCIF format (max size: 2 MB).

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Upload one or more PDB and PDBx/mmCIF files, optionally gzipped (max: 10 MB). To select multiple files, hold down Ctrl and click the left mouse button.

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Select structure database(s) for GTalign search.

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Optionally, provide an email address to receive a notification upon job completion.

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Optionally, provide a custom job description.

Search and alignment options

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Report results down to this TM-score limit. Possible values range from 0 to 1 (exclusive).

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Specify your alignment sorting preferences.

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Number of highest-scoring structure alignments and superpositions to output for each query (maximum: 1000).

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Minimum pairwise sequence similarity score for conducting structure comparison. Values ≥10 significantly impact speed. A value of 0 means all pairs are subject to further processing. The maximum value is 100.

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Minimum provisional TM-score, ranging from 0.3 to 1 (exclusive), for structure pairs to proceed to further stages. A value of 0 means all pairs are subject to further processing.

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Increase the speed of the GTalign alignment algorithm by reducing optimality. Higher values result in faster computation, with a maximum of 13.

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Remove deletion positions (gaps in the query) from the generated alignments.