Nucleic Acids Research, 2001, Vol. 29, No. 1 55-57
© 2001 Oxford University Press
A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3
Structural Genomics Group, EMBL-EBI, Cambridge CB10 1SD, UK and 1Structural and Genetic Information, CNRS UMR 1889, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
The Dali Domain Dictionary (http://www.ebi.ac.uk/dali/domain) is a numerical taxonomy of all known structures in the Protein Data Bank (PDB). The taxonomy is derived fully automatically from measurements of structural, functional and sequence similarities. Here, we report the extension of the classification to match the traditional four hierarchical levels corresponding to: (i) supersecondary structural motifs (attractors in fold space), (ii) the topology of globular domains (fold types), (iii) remote homologues (functional families) and (iv) homologues with sequence identity above 25% (sequence families). The computational definitions of attractors and functional families are new. In September 2000, the Dali classification contained 10 531 PDB entries comprising 17 101 chains, which were partitioned into five attractor regions, 1375 fold types, 2582 functional families and 3724 domain sequence families. Sequence families were further associated with 99 582 unique homologous sequences in the HSSP database, which increases the number of effectively known structures several-fold. The resulting database contains the description of protein domain architecture, the definition of structural neighbours around each known structure, the definition of structurally conserved cores and a comprehensive library of explicit multiple alignments of distantly related protein families.
* To whom correspondence should be addressed. Tel: +44 1223 494454; Fax: +44 1223 494470; Email: holm{at}ebi.ac.uk
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  E. L. Peterson, J. Kondev, J. A. Theriot, and R. Phillips Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment Bioinformatics, June 1, 2009; 25(11): 1356 - 1362. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. A.C. Beck, A. L. Jonsson, R. D. Schaeffer, K. A. Scott, R. Day, R. D. Toofanny, D. O.V. Alonso, and V. Daggett Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations Protein Eng. Des. Sel., June 1, 2008; 21(6): 353 - 368. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Malgieri, L. Russo, S. Esposito, I. Baglivo, L. Zaccaro, E. M. Pedone, B. Di Blasio, C. Isernia, P. V. Pedone, and R. Fattorusso The prokaryotic Cys2His2 zinc-finger adopts a novel fold as revealed by the NMR structure of Agrobacterium tumefaciens Ros DNA-binding domain PNAS, October 30, 2007; 104(44): 17341 - 17346. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Busch, J. Lacal, A. Martos, J. L. Ramos, and T. Krell Bacterial sensor kinase TodS interacts with agonistic and antagonistic signals PNAS, August 21, 2007; 104(34): 13774 - 13779. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Lerman and B. E. Shakhnovich Defining functional distance using manifold embeddings of gene ontology annotations PNAS, July 3, 2007; 104(27): 11334 - 11339. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Rueda, C. Ferrer-Costa, T. Meyer, A. Perez, J. Camps, A. Hospital, J. L. Gelpi, and M. Orozco A consensus view of protein dynamics PNAS, January 16, 2007; 104(3): 796 - 801. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Yu, Y.-H. Liang, E. Brostromer, J.-M. Quan, S. Panjikar, Y.-H. Dong, and X.-D. Su A Catalytic Mechanism Revealed by the Crystal Structures of the Imidazolonepropionase from Bacillus subtilis J. Biol. Chem., December 1, 2006; 281(48): 36929 - 36936. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Janner, A. V Pandey, P. E Mullis, and C. E Fluck Clinical and biochemical description of a novel CYP21A2 gene mutation 962_963insA using a new 3D model for the P450c21 protein. Eur. J. Endocrinol., July 1, 2006; 155(1): 143 - 151. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-C. Chen, Y.-C. Chang, C.-H. Lin, C.-H. Lin, and S.-H. Liaw Crystal Structure of a Bifunctional Deaminase and Reductase from Bacillus subtilis Involved in Riboflavin Biosynthesis J. Biol. Chem., March 17, 2006; 281(11): 7605 - 7613. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C.-H. Huang, W.-L. Lai, M.-H. Lee, C.-J. Chen, A. Vasella, Y.-C. Tsai, and S.-H. Liaw Crystal Structure of Glucooligosaccharide Oxidase from Acremonium strictum: A NOVEL FLAVINYLATION OF 6-S-CYSTEINYL, 8{alpha}-N1-HISTIDYL FAD J. Biol. Chem., November 18, 2005; 280(46): 38831 - 38838. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Schnell, T. Sandalova, U. Hellman, Y. Lindqvist, and G. Schneider Siroheme- and [Fe4-S4]-dependent NirA from Mycobacterium tuberculosis Is a Sulfite Reductase with a Covalent Cys-Tyr Bond in the Active Site J. Biol. Chem., July 22, 2005; 280(29): 27319 - 27328. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Espadaler, R. Aragues, N. Eswar, M. A. Marti-Renom, E. Querol, F. X. Aviles, A. Sali, and B. Oliva Detecting remotely related proteins by their interactions and sequence similarity PNAS, May 17, 2005; 102(20): 7151 - 7156. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Sandelin Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach Bioinformatics, April 1, 2005; 21(7): 1002 - 1009. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. E. Shakhnovich, E. Deeds, C. Delisi, and E. Shakhnovich Protein structure and evolutionary history determine sequence space topology Genome Res., March 1, 2005; 15(3): 385 - 392. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Casbon and M. A. S. Saqi S4: structure-based sequence alignments of SCOP superfamilies Nucleic Acids Res., January 1, 2005; 33(suppl_1): D219 - D222. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-H. Liaw, Y.-J. Chang, C.-T. Lai, H.-C. Chang, and G.-G. Chang Crystal Structure of Bacillus subtilis Guanine Deaminase: THE FIRST DOMAIN-SWAPPED STRUCTURE IN THE CYTIDINE DEAMINASE SUPERFAMILY J. Biol. Chem., August 20, 2004; 279(34): 35479 - 35485. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W.-L. Lai, L.-Y. Chou, C.-Y. Ting, R. Kirby, Y.-C. Tsai, A. H.-J. Wang, and S.-H. Liaw The Functional Role of the Binuclear Metal Center in D-Aminoacylase: ONE-METAL ACTIVATION AND SECOND-METAL ATTENUATION J. Biol. Chem., April 2, 2004; 279(14): 13962 - 13967. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Espadaler, N. Fernandez-Fuentes, A. Hermoso, E. Querol, F. X. Aviles, M. J. E. Sternberg, and B. Oliva ArchDB: automated protein loop classification as a tool for structural genomics Nucleic Acids Res., January 1, 2004; 32(90001): D185 - 188. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Agrawal, P. V. N. Dasaradhi, A. Mohmmed, P. Malhotra, R. K. Bhatnagar, and S. K. Mukherjee RNA Interference: Biology, Mechanism, and Applications Microbiol. Mol. Biol. Rev., December 1, 2003; 67(4): 657 - 685. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Poirot, E. O'Toole, and C. Notredame Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments Nucleic Acids Res., July 1, 2003; 31(13): 3503 - 3506. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T.-P. Ko, J.-J. Lin, C.-Y. Hu, Y.-H. Hsu, A. H.-J. Wang, and S.-H. Liaw Crystal Structure of Yeast Cytosine Deaminase: INSIGHTS INTO ENZYME MECHANISM AND EVOLUTION J. Biol. Chem., May 23, 2003; 278(21): 19111 - 19117. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-H. Liaw, S.-J. Chen, T.-P. Ko, C.-S. Hsu, C.-J. Chen, A. H.-J. Wang, and Y.-C. Tsai Crystal Structure of D-Aminoacylase from Alcaligenes faecalis DA1. A NOVEL SUBSET OF AMIDOHYDROLASES AND INSIGHTS INTO THE ENZYME MECHANISM J. Biol. Chem., February 7, 2003; 278(7): 4957 - 4962. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. S. Krishna, I. Majumdar, and N. V. Grishin Structural classification of zinc fingers: SURVEY AND SUMMARY Nucleic Acids Res., January 15, 2003; 31(2): 532 - 550. [Abstract] [Full Text] [PDF]
|
|