Tutorial: Using GTalign-web

Users are encouraged to refer to the Help page for a detailed overview of the services provided by GTalign-web, the GTalign web server. This tutorial provides step-by-step instructions for performing structure searches, reviewing results, and constructing multiple structure alignments.

Step 1: Upload input data

On the GTalign-web main page, upload your input data by clicking the "Upload structure file(s)" button.

For a single query structure, upload a file with one of the following extensions: .ent[.gz], .pdb[.gz], or .cif[.gz]. Upload of several files is possible. For multiple query structures, it is also possible to upload a .tar file containing the individual structure files.

Step 2: Select target structure databases

Choose structure databases (e.g., PDB, SCOPe40, UniRef30) to search against.

Step 3: Configure search options

If necessary, expand the "Search and alignment options" section and adjust additional search parameters such as the minimum TM-score threshold, sorting options, or structure/sequence similarity filters.

Step 4: Submit the job

Click the "Submit" button to place your job in the queue.

Step 5: Check job progress

As the job runs, you can monitor its progress through the displayed status updates.

Step 6: View results

Once the job is complete, links to individual results pages for each query chain and/or model will appear.

Step 7: Choose alignments to analyze

For each query, a results summary and a detailed table are displayed. The schematic alignments are colored according to TM-score values, taking into account the chosen sorting order. Clicking on the schematic alignment or a row number in the table helps access the corresponding pairwise alignment.

Step 8: Analyze pairwise alignments

Each results page provides the following information:

• Structural alignments with visual representations of secondary structure elements to assess topological similarity.
  • h: alpha helix
  • e: beta strand
  • t: turn
• Alignment statistics, including:
  • TM-scores (length-normalized) for the reference and query.
  • 2TM-scores to account for unmatched helices.
  • RMSD, identity percentage, and the number of aligned residues.
• Transformation data, rotation matrices and translation vectors, for superimposing the reference structure onto the query.

Step 9: View structure superpositons

View structure superposition after clicking on "Superposition" buttons in results table or next to alignments.

Structure superposition opens in a new tab.

Step 10: Select pairwise alignments

Select pairwise alignments from the results, either manually or by specifying criteria such as a range of TM-scores or keyword search in result descriptions.

Step 11: Construct a Multiple Sequence Alignment (MSA) from structure alignments

Based on the selected pairwise alignments, construct an MSA. The resulting MSA will be displayed and can be analyzed interactively.

Step 12: Download selected superpositions

By clicking on "Download selected superpositons" button on the results page, you can download multiple superposed structures.

Superpositions download page opens in a new tab, and after some time it is possible to download them in one ZIP file.