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Improving the consistency of domain annotation within the Conserved Domain Database

Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Jane He, Gabriele H. Marchler, Zhouxi Wang, Aron Marchler-Bauer
<span title="2015-01-01">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
Citation details: Derbyshire,M.K., Gonzales,N.R., Lu,S., et al. Improving the consistency of domain annotation within the conserved domain database (CDD).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bav012">doi:10.1093/database/bav012</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25767294">pmid:25767294</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4356950/">pmcid:PMC4356950</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uyjohnfrnjfrzjyj55me6gs5pa">fatcat:uyjohnfrnjfrzjyj55me6gs5pa</a> </span>
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CDD: NCBI's conserved domain database

Aron Marchler-Bauer, Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Farideh Chitsaz, Lewis Y. Geer, Renata C. Geer, Jane He, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu (+8 others)
<span title="2014-11-20">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
NCBI's CDD, the Conserved Domain Database, enters its 15 th year as a public resource for the annotation of proteins with the location of conserved domain footprints. Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD. We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk. We also maintain import
more &raquo; ... edures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort. The curation effort aims at increasing coverage and providing finergrained classifications of common protein domains, for which a wealth of functional and structural data has become available. CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features. CDD can be accessed at http://www.ncbi.nlm.nih.gov/Structure/ cdd/cdd.shtml.
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CDD: conserved domains and protein three-dimensional structure

Aron Marchler-Bauer, Chanjuan Zheng, Farideh Chitsaz, Myra K. Derbyshire, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu, Shennan Lu (+6 others)
<span title="2012-11-28">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
CDD, the Conserved Domain Database, is part of NCBI's Entrez query and retrieval system and is also accessible via http://www.ncbi.nlm.nih.gov/ Structure/cdd/cdd.shtml. CDD provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints. Pre-computed annotation is available via Entrez, and interactive search services accept single protein or nucleotide queries, as well as batch submissions of protein query sequences,
more &raquo; ... tilizing RPS-BLAST to rapidly identify putative matches. CDD incorporates several protein domain and full-length protein model collections, and maintains an active curation effort that aims at providing fine grained classifications for major and wellcharacterized protein domain families, as supported by available protein three-dimensional (3D) structure and the published literature. To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts.
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RefSeq: an update on prokaryotic genome annotation and curation

Daniel H Haft, Michael DiCuccio, Azat Badretdin, Vyacheslav Brover, Vyacheslav Chetvernin, Kathleen O'Neill, Wenjun Li, Farideh Chitsaz, Myra K Derbyshire, Noreen R Gonzales, Marc Gwadz, Fu Lu (+9 others)
<span title="2017-11-03">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The pipeline now finds all three formate dehydrogenase isoforms in E. coli K-12, all six selenoproteins expected in Clostridioides difficile CD196, and all eight expected in Geobacter sulfurreducens KN400  ... 
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CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

Aron Marchler-Bauer, Yu Bo, Lianyi Han, Jane He, Christopher J. Lanczycki, Shennan Lu, Farideh Chitsaz, Myra K. Derbyshire, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz (+10 others)
<span title="2016-11-29">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
NCBI's Conserved Domain Database (CDD) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints. An archive of pre-computed domain annotation is maintained for proteins tracked by NCBI's Entrez database, and live search services are offered as well. CDD curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from
more &raquo; ... providers, with representations of selected domain families that are curated in-house and organized into hierarchical classifications of functionally distinct families and sub-families. CDD also supports comparative analyses of protein families via conserved domain architectures, and a recent curation effort focuses on providing functional characterizations of distinct subfamily architectures using SPARCLE: Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi. nlm.nih.gov/Structure/cdd/cdd.shtml.
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Page 1231 of The Lancet Vol. 2, Issue 4131 [page]

<span title="1902-11-01">1902</span> <i title="ELSEVIER LTD."> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_the-lancet" style="color: black;">The Lancet </a> </i> &nbsp;
[Nov. 1, 1902. {[23) Salary Norwi K N ANT STAPFPE KDSHIRE GEN for tt i Births, Hlarriages, and BIRTH at Cairo, tl MAKRIAGES Byletts wer Mary's Reginal f at St aptain mdolyne, second daughter and Mrs.  ...  ., has heen appointed Honorary Phy sician to the Derbyshire Royal Infirmary, vice Winfred Benthall, M.B. Cantah., resigned Wuire, Artruur T., L.R.C.P., L.R.C.8.  ... 
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Page 190 of Englishwoman's Domestic Magazine Vol. 1, Issue [page]

<span title="">1852</span> <i title="Out-of-copyright"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_englishwomans-domestic-magazine" style="color: black;">Englishwoman&#39;s Domestic Magazine</a> </i> &nbsp;
(Derbyshire) Q. 3—It will tend to the happiness of both. Dick (Derbyshire) Q. 5—Thy career will be a joyous one. Emily Laora (Sleaford) Q. 9—For thy mental qualities. M. 8 (Lincolnshire) Q.  ...  K. (Islington) Q. 15—One lair and fond. II. J. (Everton) Q. 9—For delicacy and good tense. 8. D. (St.  ... 
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Page 1440 of PMLA. Publications of the Modern Language Association of America Vol. 51, Issue 4 [page]

<span title="">1936</span> <i title="Modern Language Association of America"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_pmla-publications-modern-language-assoc-of-america" style="color: black;">PMLA. Publications of the Modern Language Association of America </a> </i> &nbsp;
Ethel K., Asst. Prof. Eng., Univ. of Denver, Denver, Colo. [2075 S. High St.] Schumann, Detlev W., Assoc. Prof. Ger- manic Langs. and Lits., Brown Univ., Providence, R. I.  ...  Seeber, Edward Derbyshire, Assoc. Prof. Rom. Langs., Coll. of Charleston, Charles- ton, S. C. Seely, Frederick Franklin, Instr. Eng., Alle- gheny Coll., Meadville, Pa. Seemann, Eric, Instr.  ... 
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Page 56 of Englishwoman's Domestic Magazine Vol. 27, Issue [page]

<span title="">1879</span> <i title="Out-of-copyright"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_englishwomans-domestic-magazine" style="color: black;">Englishwoman&#39;s Domestic Magazine</a> </i> &nbsp;
K.—We cannot possibly reprint the letter.  ...  War¬ ranted the best Derbyshire make, and surpassed by none in the trade.  ... 
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Page 805 of The Gentleman's Magazine Vol. 218, Issue [page]

<span title="">1865</span> <i title="Open Court Publishing Co"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_gentlemans-magazine" style="color: black;">The Gentleman&#39;s Magazine </a> </i> &nbsp;
., of Ash- bourne, Derbyshire. At Southsea, aged 27, John Constantine, son of Major-Gen. Pester.  ...  At Brighton, Myra Harriet, dau. of the late Gen. Hugh Stacey Osborne, of Pengelly House, Cheshunt. May 11, At Charlcombe Villa, Bath, aged  ... 
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Page 432 of The Garden Vol. 107, Issue 10 [page]

<span title="">1982</span> <i title="Royal Horticultural Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_the-garden" style="color: black;">The Garden</a> </i> &nbsp;
Garage, attractive gardens approximately lA acre, wide variety of plants including many unusual shrubs. £65,(K)0. Telephone: (0M3) 862447. SUFFOLK-NORFOLK border.  ...  Myra Murby, 51 Winoisor Rd., Kew, Richmond, Surrey. EMERALD JEWELLERY We buy for cash on behalf of many of our customers who urgently require good quality Emerald and Diamond Jewellery.  ... 
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Page 1457 of Linguistics and Language Behavior Abstracts: LLBA Vol. 26, Issue 3 [page]

<span title="">1992</span> <i > <a target="_blank" rel="noopener" href="https://archive.org/details/pub_linguistics-and-language-behavior-abstracts-llba" style="color: black;">Linguistics and Language Behavior Abstracts: LLBA </a> </i> &nbsp;
G., 9205163 Denton, Robert F., 9206453 Denzer, Debra, 9205815 Deprez, Kas, 9207060 Derbyshire, William W., 92r01850, 92r01901, 92r01902 Deregowski, J.  ...  920611 Dumitresku, Mariya, 9206937, 92r02432 Dumont, Céline, 9206405 Dunalewicz, Jolanta, 92r02256 Dunbar, Stephen, 9205169 Dunkel, Patricia, 9205525 Dunn, John A., 9206570 Dunn, Judy, 9206993 Dunn, Myra  ... 
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Page 907 of The Lancet Vol. 1, Issue 3271 [page]

<span title="1886-05-08">1886</span> <i title="ELSEVIER LTD."> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_the-lancet" style="color: black;">The Lancet </a> </i> &nbsp;
—On the 5th inst., at Matheson-road, West K nm, W., James Thompson, M.D. (formerly of Avenue House, pone ey er, Sussex, John N.B.  ...  Derbyshire, Emil ia Laird, the beloved ried Alfred wner, L.R.C.P.Lond., M. R.0.8., and daughter of William Clowes, Hsq., of 86, Holland-road, Kensington (Chancery Registrar), aged 28. CumMine.  ... 
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Page 568 of None Vol. 99, Issue 2583 [page]

<span title="1905-04-29">1905</span> <i title="Out-of-copyright"> <a target="_blank" rel="noopener" href="https://archive.org/details/None" style="color: black;">None</a> </i> &nbsp;
Burleigh, 25. 6d, Ground Ivy (Myra Swan). Brown, Langham. 6s. HIsTORY The Progress of Hellenism in Alexander’s Empire (John Pentland Mahaffy). Unwin. 5s.  ...  Allenson. 2s. 6d, i TRAVEL Highways and Byways in Derbyshire (J. Nelly Erichsen). Macmillan. 6s. Five Years in a Persian Town (Napier Malcolm), tos. 6d. net; From the Cape to the Zambesi (G. T.  ... 
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: Caye Caulker: Economic Success in a Belizean Fishing Village . Anne Sutherland. ; Fisher Folk: Two Communities on Chesapeake Bay . Carolyn Ellis. ; Texas Shrimpers: Community, Capitalism, and the Sea . Robert Lee Maril. ; Perceptions and Preferences for Marine Fish: A Study of Recreational Fishermen in the Southeast . Jeffrey C. Johnson, David Griffith. ; Transfer Patterns in Alaskan Limited Entry Fisheries . Steve Langdon

Shirley J. Fiske
<span title="">1987</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7wswypm2nzhozb3avivbbjosgu" style="color: black;">American Anthropologist</a> </i> &nbsp;
: Yeti, Sasquatch and the Neanderthal Enigma, Myra Shackley, book reviewed by Kathleen J. Reichs, 508 Stone Age Prehistory: Studies in Memory of Charies McBurney, G. N. Bailey and P.  ...  Davenport, William H., 177 Davis, Boyd H., 182 Davis, William G., 9 Day, Michael H., 971 Dayley, Jon P., 190 D’ Azevedo, Warren L., 738 Delson, Eric, 200 den Otter, Elisabeth, 156 Dentan, Robert Knox, 356 Derbyshire  ... 
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