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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.

Query chains shorter than 20 or longer than 4000 residues or nucleotides will not be processed.

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.