Nucleic Acids Research, 2005, Vol. 33, Database issue D192-D196
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
CDD: a Conserved Domain Database for protein classification
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
* To whom correspondence should be addressed. Tel: +1 301 435 4919; Fax: +1 301 480 9241; Email: bauer{at}ncbi.nlm.nih.gov
Received September 22, 2004; Accepted October 5, 2004
The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed®, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein–protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system.
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I. E. Gentle, A. J. Perry, F. H. Alcock, V. A. Likic, P. Dolezal, E. T. Ng, A. W. Purcell, M. McConnville, T. Naderer, A.-L. Chanez, et al. Conserved Motifs Reveal Details of Ancestry and Structure in the Small TIM Chaperones of the Mitochondrial Intermembrane Space Mol. Biol. Evol., May 1, 2007; 24(5): 1149 - 1160. [Abstract] [Full Text] [PDF]
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U. Wegmann, M. O'Connell-Motherway, A. Zomer, G. Buist, C. Shearman, C. Canchaya, M. Ventura, A. Goesmann, M. J. Gasson, O. P. Kuipers, et al. Complete Genome Sequence of the Prototype Lactic Acid Bacterium Lactococcus lactis subsp. cremoris MG1363 J. Bacteriol., April 15, 2007; 189(8): 3256 - 3270. [Abstract] [Full Text] [PDF]
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D. Przybylski and B. Rost Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments Nucleic Acids Res., April 1, 2007; 35(7): 2238 - 2246. [Abstract] [Full Text] [PDF]
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R. Sukackaite, A. Lagunavicius, K. Stankevicius, C. Urbanke, C. Venclovas, and V. Siksnys Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family Nucleic Acids Res., April 1, 2007; 35(7): 2377 - 2389. [Abstract] [Full Text] [PDF]
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K. Schult, K. Meierhoff, S. Paradies, T. Toller, P. Wolff, and P. Westhoff The Nuclear-Encoded Factor HCF173 Is Involved in the Initiation of Translation of the psbA mRNA in Arabidopsis thaliana PLANT CELL, April 1, 2007; 19(4): 1329 - 1346. [Abstract] [Full Text] [PDF]
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D. A. Rodionov, O. V. Kurnasov, B. Stec, Y. Wang, M. F. Roberts, and A. L. Osterman Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate PNAS, March 13, 2007; 104(11): 4279 - 4284. [Abstract] [Full Text] [PDF]
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H. Shindou, D. Hishikawa, H. Nakanishi, T. Harayama, S. Ishii, R. Taguchi, and T. Shimizu A Single Enzyme Catalyzes Both Platelet-activating Factor Production and Membrane Biogenesis of Inflammatory Cells: CLONING AND CHARACTERIZATION OF ACETYL-CoA:LYSO-PAF ACETYLTRANSFERASE J. Biol. Chem., March 2, 2007; 282(9): 6532 - 6539. [Abstract] [Full Text] [PDF]
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Y. Nakagawa, T. Katagiri, K. Shinozaki, Z. Qi, H. Tatsumi, T. Furuichi, A. Kishigami, M. Sokabe, I. Kojima, S. Sato, et al. Arabidopsis plasma membrane protein crucial for Ca2+ influx and touch sensing in roots PNAS, February 27, 2007; 104(9): 3639 - 3644. [Abstract] [Full Text] [PDF]
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B. E. Snow, M. Mateyak, J. Paderova, A. Wakeham, C. Iorio, V. Zakian, J. Squire, and L. Harrington Murine Pif1 Interacts with Telomerase and Is Dispensable for Telomere Function In Vivo Mol. Cell. Biol., February 1, 2007; 27(3): 1017 - 1026. [Abstract] [Full Text] [PDF]
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S. Fresno, N. Jimenez, R. Canals, S. Merino, M. M. Corsaro, R. Lanzetta, M. Parrilli, G. Pieretti, M. Regue, and J. M. Tomas A Second Galacturonic Acid Transferase Is Required for Core Lipopolysaccharide Biosynthesis and Complete Capsule Association with the Cell Surface in Klebsiella pneumoniae J. Bacteriol., February 1, 2007; 189(3): 1128 - 1137. [Abstract] [Full Text] [PDF]
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T. Komatsuda, M. Pourkheirandish, C. He, P. Azhaguvel, H. Kanamori, D. Perovic, N. Stein, A. Graner, T. Wicker, A. Tagiri, et al. Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene PNAS, January 23, 2007; 104(4): 1424 - 1429. [Abstract] [Full Text] [PDF]
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D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, et al. Database resources of the National Center for Biotechnology Information Nucleic Acids Res., January 12, 2007; 35(suppl_1): D5 - D12. [Abstract] [Full Text] [PDF]
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A. G. Jegga, S. Gowrisankar, J. Chen, and B. J. Aronow PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease Nucleic Acids Res., January 12, 2007; 35(suppl_1): D700 - D706. [Abstract] [Full Text] [PDF]
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