Dali Downloads
Available Downloads
The Dali Database contains structural alignments of PDB90 versus the full PDB using
DaliLite. The data can be viewed interactively
here, or downloaded in its entirety below.
The SQL dump files are very large, up to 450MB. Therefore, when you click a link to download a file, there may be
a short delay before the download dialogue box pops up. Please do not re-click the link,
but wait for the download box to appear.
The Dali Database as SQL dump*:
DaliLite standalone program
*SQL Dumps - format descriptions
1) Pairwise scores, table dalidb_dccp
The columns are:
- unique alignment identifier
- PDB code plus chain identifier of query structure
- PDB code plus chain identifier of sbjct (matching structure)
- Z-score - the raw score is normalized taking into account the size of the matching domains [5]
2) Pairwise alignments, table dalidb_segments
The columns are:
- unique alignment identifier
- first residue of an aligned block in the query protein
- first residue in that block in the subject protein
- length of that block
Residues are numbered sequentially starting from 1.
COPYRIGHT
All rights reserved, including copyrights. Free academic use. No commercial use. No incorporation into other databases.
References
- Heger A, Holm L (2003) Exhaustive enumeration of protein domain families. J Mol Biol 328, 749-767.
- Holm L, Sander C (1996) Mapping the protein universe. Science 273, 595-603.
- Holm L, Sander C (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
- Holm L, Sander C (1998) Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics 14, 423-429.
- Holm L, Sander C (1998) Dictionary of recurrent domains in protein structures. Proteins 33, 88-96. PDF
- Holm L, Kaariainen S, Rosenstrom P, Schenkel A. (2008) Searching protein structure databases with DaliLite v.3. Bioinformatics 24, 2780-2781.