Dali server (original) (raw)

The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB). In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences.

Check queue status here. Megausers please consider downloading the standalone program.

You can perform three types of database searches:

• Heuristic PDB search - compares one query structure against those in the Protein Data Bank
• Exhaustive PDB25 search - compares one query structure against a representative subset of the Protein Data Bank
• Hierarchical AF-DB search - compares one query structure against a species subset of the AlphaFold Database v2
• beta testing:AF-DB heuristic - search AlphaFold Database v2 in minutes

and two types of structure comparisons of user selected structures:

• Pairwise structure comparison - compares one query structure against those specified by the user
• All against all structure comparison - returns a structural similarity dendrogram for a set of structures specified by the user

Citation:

1. Holm L, Laiho A, Toronen P, Salgado M (2023) DALI shines a light on remote homologs: one hundred discoveries. Protein Science 23, e4519