Nucleic Acids Research, Vol 26, Issue 1 316-319, Copyright © 1998 by Oxford University Press
L Holm and C Sander
The FSSP database and its new supplement, the Dali Domain Dictionary,
present a continuously updated classification of all known 3D protein
structures. The classification is derived using an automatic structure
alignment program (Dali) for the all-against-all comparison of structures
in the Protein Data Bank. From the resulting enumeration of structural
neighbours (which form a surprisingly continuous distribution in fold
space) we derive a discrete fold classification in three steps: (i)
sequence-related families are covered by a representative set of protein
chains; (ii) protein chains are decomposed into structural domains based on
the recurrence of structural motifs; (iii) folds are defined as tight
clusters of domains in fold space. The fold classification, domain
definitions and test sets for sequence-structure alignment (threading) are
accessible on the web at www.embl-ebi.ac.uk/dali . The web interface
provides a rich network of links between neighbours in fold space, between
domains and proteins, and between structures and sequences leading, for
example, to a database of explicit multiple alignments of protein families
in the twilight zone of sequence similarity. The Dali/FSSP organization of
protein structures provides a map of the currently known regions of the
protein universe that is useful for the analysis of folding principles, for
the evolutionary unification of protein families and for maximizing the
information return from experimental structure determination.
ARTICLES
Touring protein fold space with Dali/FSSP
European Molecular Biology Laboratory, European Bioinformatics Institute, Genome Campus, Cambridge CB10 1SD, UK. holm@embl-ebi.ac.uk
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S. Doublie, V. Bandaru, J. P. Bond, and S. S. Wallace The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity PNAS, July 13, 2004; 101(28): 10284 - 10289. [Abstract] [Full Text] [PDF]
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 S. D. Patel, M. W. Rajala, L. Rossetti, P. E. Scherer, and L. Shapiro Disulfide-Dependent Multimeric Assembly of Resistin Family Hormones Science, May 21, 2004; 304(5674): 1154 - 1158. [Abstract] [Full Text] [PDF]
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F. Alberto, C. Bignon, G. Sulzenbacher, B. Henrissat, and M. Czjzek The Three-dimensional Structure of Invertase ({beta}-Fructosidase) from Thermotoga maritima Reveals a Bimodular Arrangement and an Evolutionary Relationship between Retaining and Inverting Glycosidases J. Biol. Chem., April 30, 2004; 279(18): 18903 - 18910. [Abstract] [Full Text] [PDF]
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A. Y. Lau and D. I. Chasman Functional classification of proteins and protein variants PNAS, April 27, 2004; 101(17): 6576 - 6581. [Abstract] [Full Text] [PDF]
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R. C. Edgar MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res., March 19, 2004; 32(5): 1792 - 1797. [Abstract] [Full Text] [PDF]
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J. A. Bauer, E. M. Bennett, T. P. Begley, and S. E. Ealick Three-dimensional Structure of YaaE from Bacillus subtilis, a Glutaminase Implicated in Pyridoxal-5'-phosphate Biosynthesis J. Biol. Chem., January 23, 2004; 279(4): 2704 - 2711. [Abstract] [Full Text] [PDF]
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G. Golan, D. Shallom, A. Teplitsky, G. Zaide, S. Shulami, T. Baasov, V. Stojanoff, A. Thompson, Y. Shoham, and G. Shoham Crystal Structures of Geobacillus stearothermophilus {alpha}-Glucuronidase Complexed with Its Substrate and Products: MECHANISTIC IMPLICATIONS J. Biol. Chem., January 23, 2004; 279(4): 3014 - 3024. [Abstract] [Full Text] [PDF]
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R. C. Edgar Local homology recognition and distance measures in linear time using compressed amino acid alphabets Nucleic Acids Res., January 16, 2004; 32(1): 380 - 385. [Abstract] [Full Text] [PDF]
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H. Pang, M. Bartlam, Q. Zeng, H. Miyatake, T. Hisano, K. Miki, L.-L. Wong, G. F. Gao, and Z. Rao Crystal Structure of Human Pirin: AN IRON-BINDING NUCLEAR PROTEIN AND TRANSCRIPTION COFACTOR J. Biol. Chem., January 9, 2004; 279(2): 1491 - 1498. [Abstract] [Full Text] [PDF]
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R. A. Selvam and R. Sasidharan DomIns: a web resource for domain insertions in known protein structures Nucleic Acids Res., January 1, 2004; 32(90001): D193 - 195. [Abstract] [Full Text] [PDF]
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H.-J. Yeo, Q. Yuan, M. R. Beck, C. Baron, and G. Waksman Structural and functional characterization of the VirB5 protein from the type IV secretion system encoded by the conjugative plasmid pKM101 PNAS, December 23, 2003; 100(26): 15947 - 15952. [Abstract] [Full Text] [PDF]
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A. Sathyamurthy, M. D. Allen, A. G. Murzin, and M. Bycroft Crystal Structure of the Malignant Brain Tumor (MBT) Repeats in Sex Comb on Midleg-like 2 (SCML2) J. Biol. Chem., November 21, 2003; 278(47): 46968 - 46973. [Abstract] [Full Text] [PDF]
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R. Ishii, O. Nureki, and S. Yokoyama Crystal Structure of the tRNA Processing Enzyme RNase PH from Aquifex aeolicus J. Biol. Chem., August 22, 2003; 278(34): 32397 - 32404. [Abstract] [Full Text] [PDF]
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C.-C. Chou, T.-W. Lin, C.-Y. Chen, and A. H.-J. Wang Crystal Structure of the Hyperthermophilic Archaeal DNA-Binding Protein Sso10b2 at a Resolution of 1.85 Angstroms J. Bacteriol., July 15, 2003; 185(14): 4066 - 4073. [Abstract] [Full Text] [PDF]
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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]
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C. Brooksbank, E. Camon, M. A. Harris, M. Magrane, M. J. Martin, N. Mulder, C. O'Donovan, H. Parkinson, M. A. Tuli, R. Apweiler, et al. The European Bioinformatics Institute's data resources Nucleic Acids Res., January 1, 2003; 31(1): 43 - 50. [Abstract] [Full Text] [PDF]
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R. A. Chiang, E. C. Meng, C. C. Huang, T. E. Ferrin, and P. C. Babbitt The Structure Superposition Database Nucleic Acids Res., January 1, 2003; 31(1): 505 - 510. [Abstract] [Full Text] [PDF]
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E. L. Borths, K. P. Locher, A. T. Lee, and D. C. Rees The structure of Escherichia coli BtuF and binding to its cognate ATP binding cassette transporter PNAS, December 24, 2002; 99(26): 16642 - 16647. [Abstract] [Full Text] [PDF]
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S. B. Williams, I. Vakonakis, S. S. Golden, and A. C. LiWang Structure and function from the circadian clock protein KaiA of Synechococcus elongatus: A potential clock input mechanism PNAS, November 26, 2002; 99(24): 15357 - 15362. [Abstract] [Full Text] [PDF]
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F. X. Gomis-Ruth, A. Bayes, G. Sotiropoulou, G. Pampalakis, T. Tsetsenis, V. Villegas, F. X. Aviles, and M. Coll The Structure of Human Prokallikrein 6 Reveals a Novel Activation Mechanism for the Kallikrein Family J. Biol. Chem., July 19, 2002; 277(30): 27273 - 27281. [Abstract] [Full Text] [PDF]
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U. Padmanabhan, S. Dasgupta, B. B. Biswas, and D. Dasgupta High Affinity Association of myo-Inositol Trisphosphates with Phytase and Its Effect upon the Catalytic Potential of the Enzyme J. Biol. Chem., November 16, 2001; 276(47): 43635 - 43644. [Abstract] [Full Text] [PDF]
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 L. Aravind and E. V. Koonin Prokaryotic Homologs of the Eukaryotic DNA-End-Binding Protein Ku, Novel Domains in the Ku Protein and Prediction of a Prokaryotic Double-Strand Break Repair System Genome Res., August 1, 2001; 11(8): 1365 - 1374. [Abstract] [Full Text] [PDF]
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I. N. Shindyalov and P. E. Bourne A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm Nucleic Acids Res., January 1, 2001; 29(1): 228 - 229. [Abstract] [Full Text] [PDF]
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D. Lang, R. Thoma, M. Henn-Sax, R. Sterner, and M. Wilmanns Structural Evidence for Evolution of the beta /alpha Barrel Scaffold by Gene Duplication and Fusion Science, September 1, 2000; 289(5484): 1546 - 1550. [Abstract] [Full Text]
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S.-J. Cho, M. G. Lee, J. K. Yang, J. Y. Lee, H. K. Song, and S. W. Suh Crystal structure of Escherichia coli CyaY protein reveals a previously unidentified fold for the evolutionarily conserved frataxin family PNAS, July 19, 2000; (2000) 160270897. [Abstract] [Full Text]
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H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne The Protein Data Bank Nucleic Acids Res., January 1, 2000; 28(1): 235 - 242. [Abstract] [Full Text] [PDF]
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S. E. Brenner, P. Koehl, and M. Levitt The ASTRAL compendium for protein structure and sequence analysis Nucleic Acids Res., January 1, 2000; 28(1): 254 - 256. [Abstract] [Full Text] [PDF]
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