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.

News: 22.5.2025 - a standalone program for searching AFDB2 published.

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

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



AF-DB comparison

Do hierarchical search of query structure against AlphaFold database (AF-DB).

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 - Select target organism


The first release of AF-DB covers the human proteome and the proteomes of several other key organisms. Searches are limited to one organism, because we use a slow systematic search without shortcuts.



STEP 3 - 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 4 - 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

... map domain families to structural alignments

... 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 (2020) DALI and the Persistence of Protein Shape. Protein Science 29, 128-140.
  2. Hasegawa H, Holm L (2009) Advances and pitfalls of protein structural alignment. Curr. Opin. Struct. Biol. 19, 381-389.
  3. Holm L, Sander C (1996) Mapping the protein universe. Science 273, 595-603
  4. Holm L, Sander C (1995) Dali: a network tool for protein structure comparison. TiBS 20:478-480

Methods:

  1. Liu H, Laiho A, Toronen P, Holm L (2025) 3-D substructure search by transitive closure in AlphaFold Database. Protein Science 34:e70169.
  2. Holm L (2022) Dali server: structural unification of protein families. Nucleic Acids Research 50, W210-W215
  3. Holm L (2020) Using Dali for Protein Structure Comparison. In: Gáspári Z. (eds) Structural Bioinformatics. Methods in Molecular Biology, vol 2112. Humana, New York, NY, pp. 29-42
  4. Holm L, Laakso LM (2016) Dali server update. Nucleic acids research 44 (W1), W351-W355.
  5. Holm L, Rosenström P (2010) Dali server: conservation mapping in 3D. Nucl. Acids Res. 38, W545-549.
  6. Holm L, Kääriäinen S, Rosenström P, Schenkel A (2008) Searching protein structure databases with DaliLite v.3. Bioinformatics 24, 2780-2781.
  7. Holm L, Park J (2000) DaliLite workbench for protein structure comparison. Bioinformatics 16, 566-567
  8. Holm L, Sander C (1998) Dictionary of recurrent domains in protein structures. Proteins 33, 88-96
  9. Holm L, Sander C (1996) Alignment of three-dimensional protein structures: network server for database searching. Meth Enz. 266:653-662
  10. Holm L, Sander C (1995) Fast protein structure database searches at 90 % reliability. ISMB 3, 179-187
  11. Holm L, Sander C (1994) Parser for protein folding units. Proteins 19, 256-268
  12. Holm L, Sander C (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138
  13. 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

Classification:

  1. Holm L (2019) Benchmarking fold detection by DaliLite v.5. Bioinformatics 35, 5326-5327.
  2. 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
  3. Dietmann S, Holm L (2001) Identification of homology in protein structure classification. Nature Structural Biology 8, 953-957
  4. Holm L, Sander C (1999) Protein folds and families: sequence and structure alignments. Nucl Acids Res 27, 244-247
  5. Holm L, Sander C (1998) Touring protein fold space with Dali/FSSP. Nucl Acids Res 26, 316-319
  6. Holm L, Sander C (1997) Decision support system for the evolutionary classification of protein structures. ISMB 5, 140-146
  7. Holm L, Sander C (1997) New structure--novel fold? Structure 5, 165-171
  8. Holm L, Sander C (1997) Dali/FSSP classification of three-dimensional protein folds. Nucl Acids Res 25, 231-234
  9. Holm L, Sander C (1996) The FSSP database: fold classification based on structure-structure alignment of proteins. Nucl Acids Res 24, 206-209
  10. Holm L, Sander C (1994) The FSSP database of structurally aligned protein fold families. Nucl. Acids Res. 22, 3600-3609

Discoveries:

  1. Holm L, Laiho A, Toronen P, Salgado M (2023) DALI shines a light on remote homologs: one hundred discoveries. Protein Science 23, e4519
  2. Holm L, Sander C (1997) Enzyme HIT. Trends Biochem 22, 116-117
  3. Holm L, Sander C (1997) An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins 28, 72-82
  4. Holm L, Sander C (1995) DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily. Trends Biochem 20:345-347
  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, 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
  7. 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
  8. Holm L, Sander C (1994) Structural similarity between plant endochitinase and lysozymes from animals and phage: an evolutionary connection. FEBS Lett. 340, 129-132
  9. Holm L, Sander C (1993) Globin fold in a bacterial toxin. Nature 361, 309

Data

Preprocessed AlphaFold Database for use with DaliLite.v5 (last update 21 February 2025)
PDB25 and other PDB subsets
scope-140 benchmark

Software

DaliLite has been tested on Red Hat Linux operating system, gcc 4.8.5 and mpirun (Open MPI) 1.10.7.

DaliLite.v5 (last update 11 April 2025)