Dali server (original) (raw)

Protein Structure Database Searching by DaliLite v. 3

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). You receive an email notification when the search has finished. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences.

Requests can also be submitted by e-mail to dali-server at helsinki dot fi. The body of the e-mail message must contain atomic coordinates in PDB format.

If you want to know the structural neighbours of a protein already in the Protein Data Bank (PDB), you can find them in the Dali Database.

If you want to superimpose two particular structures, you can do it in the pairwise DaliLite server.

Most jobs finish within an hour, but if a queue builds up, then it takes longer.

Example

PDB search results for epidermal growth factor 1egf.Tutorial

Notes

• This server runs DaliLite v.3 in -q mode. Academic users may download the DaliLite program for local use.
• This server takes as input the atomic coordinates of a protein structure. Your file need only contain ATOM/HETATM entries, although full PDB format files are fine. The structure must contain at least all backbone atoms (N, CA, C, O). If you have only the CA trace, use the MaxSprout server to generate full coordinates. The minimum chain length is 30 residues.
• The query structure is renamed mol1 in results.
• The URL of the results page is difficult to guess without knowledge of the input.
• Results are deleted after two weeks.

Statistics

• Usage
• PDB

Reference

Holm L, Kaariainen S, Rosenstrom P, Schenkel A. (2008) Searching protein structure databases with DaliLite v.3.
Bioinformatics 24, 2780-2781.