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.

You can perform four types of structure comparisons:

  • 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
  • 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. Liisa Holm; Laura M. Laakso (2016) Dali server update. Nucleic acids research 44 (W1), W351-W355.

PDB search

Compare query structure against Protein Data Bank.

STEP 1 - Enter your query protein structure


Structures may be specified by concatenating the PDB identifier (4 characters) and a chain identifier (1 character) or, alternatively, you may upload a PDB file.

OR upload file

STEP 2 - Optional data


You may leave an e-mail address for notification when the job has finished. The job title is used as subject heading in the e-mail.




STEP 3 - Submit your job



If the same structure has been submitted recently, you will be redirected to the result page of the previous instance.

PDB25 comparison

Do exhaustive pairwise comparisons of query structure against PDB25 subset Protein Data Bank. The query structure must have at least three secondary structure elements.

STEP 1 - Enter your query protein structure


Structures may be specified by concatenating the PDB identifier (4 characters) and a chain identifier (1 character) or, alternatively, you may upload a PDB file.

OR upload file

STEP 2 - Optional data


You may leave an e-mail address for notification when the job has finished. The job title is used as subject heading in the e-mail.




STEP 3 - Submit your job



If the same structure has been submitted recently, you will be redirected to the result page of the previous instance.

Pairwise structure comparison

Compare first structure against second structure.

STEP 1 - Enter your first protein structure


Structures may be specified by concatenating the PDB identifier (4 characters) and a chain identifier (1 character) or, alternatively, you may upload a PDB file.

OR upload file

STEP 2 - Enter your second protein structures


Use the +/- buttons to create input fields. The maximum number of input structures is 10.


STEP 3 - Optional data



STEP 4 - Submit your job



All against all structure comparison

STEP 1 - Enter your input protein structures


Use the +/- buttons to create input fields. Structures may be specified by concatenating the PDB identifier (4 characters) and a chain identifier (1 character) or, alternatively, you may upload a PDB file. PDB files should be entered before PDB identifiers. The maximum number of input structures is 64. If your input set consists only of structures in the PDB, you can use this alternative submission form.



STEP 2 - Optional data


You may leave an e-mail address for notification when the job has finished. The job title is used as subject heading in the e-mail.




STEP 3 - Submit your job


You can ...

... generate structural trees

... perform all against all structure comparisons of up to 64 proteins

... project high-dimensional structure space to a plane

... map structural and sequence variation to 3D structures

... compare structurally aligned sequence logos
The images above show an analysis of protein structures representing the amidohydrolase and PHP superfamilies (live example).

Reviews:

  1. Holm L, Sander C (1995) Dali: a network tool for protein structure comparison. TiBS 20:478-480
  2. Holm L, Sander C (1996) Mapping the protein universe. Science 273, 595-603
  3. Hasegawa H, Holm L (2009) Advances and pitfalls of protein structural alignment. Curr. Opin. Struct. Biol. 19, 381-389.

Methods:

  1. Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G (1992) A database of protein structure families with similar folding motifs. Protein Science 1:1691-1698
  2. Holm L, Sander C (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138
  3. Holm L, Sander C (1994) Parser for protein folding units. Proteins 19, 256-268
  4. Holm L, Sander C (1995) Fast protein structure database searches at 90 % reliability. ISMB 3, 179-187
  5. Holm L, Sander C (1996) Alignment of three-dimensional protein structures: network server for database searching. Meth Enz. 266:653-662
  6. Holm L, Sander C (1998) Dictionary of recurrent domains in protein structures. Proteins 33, 88-96
  7. Holm L, Park J (2000) DaliLite workbench for protein structure comparison. Bioinformatics 16, 566-567
  8. Holm L, Kääriäinen S, Rosenström P, Schenkel A (2008) Searching protein structure databases with DaliLite v.3. Bioinformatics 24, 2780-2781.
  9. Holm L, Rosenström P (2010) Dali server: conservation mapping in 3D. Nucl. Acids Res. 38, W545-549.
  10. Holm L, Laakso LM (2016) Dali server update. Nucleic acids research 44 (W1), W351-W355.

Classification:

  1. Holm L, Sander C (1994) The FSSP database of structurally aligned protein fold families. Nucl. Acids Res. 22, 3600-3609
  2. Holm L, Sander C (1996) The FSSP database: fold classification based on structure-structure alignment of proteins. Nucl Acids Res 24, 206-209
  3. Holm L, Sander C (1997) Dali/FSSP classification of three-dimensional protein folds. Nucl Acids Res 25, 231-234
  4. Holm L, Sander C (1997) New structure--novel fold? Structure 5, 165-171
  5. Holm L, Sander C (1997) Decision support system for the evolutionary classification of protein structures. ISMB 5, 140-146
  6. Holm L, Sander C (1998) Touring protein fold space with Dali/FSSP. Nucl Acids Res 26, 316-319
  7. Holm L, Sander C (1999) Protein folds and families: sequence and structure alignments. Nucl Acids Res 27, 244-247
  8. Dietmann S, Holm L (2001) Identification of homology in protein structure classification. Nature Structural Biology 8, 953-957
  9. Dietmann S, Park J, Notredame C, Heger A, Lappe M, Holm L (2001) A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucl Acids Res 29, 55-57

Discoveries:

  1. Holm L, Sander C (1993) Globin fold in a bacterial toxin. Nature 361, 309
  2. Holm L, Sander C (1994) Structural similarity between plant endochitinase and lysozymes from animals and phage: an evolutionary connection. FEBS Lett. 340, 129-132
  3. Holm L, Murzin A, Sander C (1994) Three sisters, different names: 3alpha,20beta-hydroxysteroid dehydrogenase, dihydropteridine reductase and UDP-galactose 4-epimerase. Nature Structural Biology 1, 146-147
  4. Holm L, Sander C, Ruterjans H, Schnarr M, Fogh R, Boelens R, Kaptein R (1994) LexA repressor and iron-uptake regulator from E. coli: new members of the CAP-like DNA-binding domain superfamily. Prot. Engin. 7, 1449-1453
  5. Holm L, Sander C (1995) Evolutionary link between glycogen phosphorylase and a DNA modifying enzyme. EMBO J. 14, 1287-1293
  6. Holm L, Sander C (1995) DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily. Trends Biochem 20:345-347
  7. Holm L, Sander C (1997) An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins 28, 72-82
  8. Holm L, Sander C (1997) Enzyme HIT. Trends Biochem 22, 116-117
Tutorial
DaliLite.v4
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