CDD/SPARCLE: the conserved domain database in 2020

被引：1954

作者：

Lu, Shennan ^{[1
]}

Wang, Jiyao ^{[1
]}

Chitsaz, Farideh ^{[1
]}

Derbyshire, Myra K. ^{[1
]}

Geer, Renata C. ^{[1
]}

Gonzales, Noreen R. ^{[1
]}

Gwadz, Marc ^{[1
]}

Hurwitz, David, I ^{[1
]}

Marchler, Gabriele H. ^{[1
]}

Song, James S. ^{[1
]}

Thanki, Narmada ^{[1
]}

Yamashita, Roxanne A. ^{[1
]}

Yang, Mingzhang ^{[1
]}

Zhang, Dachuan ^{[1
]}

Zheng, Chanjuan ^{[1
]}

Lanczycki, Christopher J. ^{[1
]}

Marchler-Bauer, Aron ^{[1
]}

机构：

[1] Natl Ctr Biotechnol Informat, Natl Lib Med, NIH, Bldg 38 A,Room 8N805,8600 Rockville Pike, Bethesda, MD 20894 USA

来源：

NUCLEIC ACIDS RESEARCH | 2020年 / 48卷 / D1期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/nar/gkz991

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

As NLM's Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, CDD curation staff continues to develop hierarchical classifications of widely distributed protein domain families, and to record conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular research. CDD offers both an archive of pre-computed domain annotations as well as live search services for both single protein or nucleotide queries and larger sets of protein query sequences. CDD staff has continued to characterize protein families via conserved domain architectures and has built up a significant corpus of curated domain architectures in support of naming bacterial proteins in RefSeq. These architecture definitions are available via SPARCLE, the Subfamily Protein Architecture Labeling Engine.

引用

页码：D265 / D268

页数：4

共 11 条

[1] The Pfam protein families database in 2019
El-Gebali, Sara
Mistry, Jaina
Bateman, Alex
Eddy, Sean R.
Luciani, Aurelien
Potter, Simon C.
Qureshi, Matloob
Richardson, Lorna J.
Salazar, Gustavo A.
Smart, Alfredo
Sonnhammer, Erik L. L.
Hirsh, Layla
Paladin, Lisanna
Piovesan, Damiano
Tosatto, Silvio C. E.
Finn, Robert D.
[J]. NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) : D427 - D432
[2] CDART: Protein homology by domain architecture
Geer, LY
Domrachev, M
Lipman, DJ
Bryant, SH
[J]. GENOME RESEARCH, 2002, 12 (10) : 1619 - 1623
[3] RefSeq: an update on prokaryotic genome annotation and curation
Haft, Daniel H.
DiCuccio, Michael
Badretdin, Azat
Brover, Vyacheslav
Chetvernin, Vyacheslav
O'Neill, Kathleen
Li, Wenjun
Chitsaz, Farideh
Derbyshire, Myra K.
Gonzales, Noreen R.
Gwadz, Marc
Lu, Fu
Marchler, Gabriele H.
Song, James S.
Thanki, Narmada
Yamashita, Roxanne A.
Zheng, Chanjuan
Thibaud-Nissen, Francoise
Geer, Lewis Y.
Marchler-Bauer, Aron
Pruitt, Kim D.
[J]. NUCLEIC ACIDS RESEARCH, 2018, 46 (D1) : D851 - D860
[4] TIGRFAMs and Genome Properties in 2013
Haft, Daniel H.
Selengut, Jeremy D.
Richter, Roland A.
Harkins, Derek
Basu, Malay K.
Beck, Erin
[J]. NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) : D387 - D395
[5] The National Center for Biotechnology Information's Protein Clusters Database
Klimke, William
Agarwala, Richa
Badretdin, Azat
Chetvernin, Slava
Ciufo, Stacy
Fedorov, Boris
Kiryutin, Boris
O'Neill, Kathleen
Resch, Wolfgang
Resenchuk, Sergei
Schafer, Susan
Tolstoy, Igor
Tatusova, Tatiana
[J]. NUCLEIC ACIDS RESEARCH, 2009, 37 : D216 - D223
[6] 20 years of the SMART protein domain annotation resource
Letunic, Ivica
Bork, Peer
[J]. NUCLEIC ACIDS RESEARCH, 2018, 46 (D1) : D493 - D496
[7] CDD: a database of conserved domain alignments with links to domain three-dimensional structure
Marchler-Bauer, A
Panchenko, AR
Shoemaker, BA
Thiessen, PA
Geer, LY
Bryant, SH
[J]. NUCLEIC ACIDS RESEARCH, 2002, 30 (01) : 281 - 283
[8] CD-Search: protein domain annotations on the fly
Marchler-Bauer, A
Bryant, SH
[J]. NUCLEIC ACIDS RESEARCH, 2004, 32 : W327 - W331
[9] CDD/SPARCLE: functional classification of proteins via subfamily domain architectures
Marchler-Bauer, Aron
Bo, Yu
Han, Lianyi
He, Jane
Lanczycki, Christopher J.
Lu, Shennan
Chitsaz, Farideh
Derbyshire, Myra K.
Geer, Renata C.
Gonzales, Noreen R.
Gwadz, Marc
Hurwitz, David I.
Lu, Fu
Marchler, Gabriele H.
Song, James S.
Thanki, Narmada
Wang, Zhouxi
Yamashita, Roxanne A.
Zhang, Dachuan
Zheng, Chanjuan
Geer, Lewis Y.
Bryant, Stephen H.
[J]. NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) : D200 - D203
[10] InterPro in 2019: improving coverage, classification and access to protein sequence annotations
Mitchell, Alex L.
Attwood, Teresa K.
Babbitt, Patricia C.
Blum, Matthias
Bork, Peer
Bridge, Alan
Brown, Shoshana D.
Chang, Hsin-Yu
El-Gebali, Sara
Fraser, Matthew I.
Gough, Julian
Haft, David R.
Huang, Hongzhan
Letunic, Ivica
Lopez, Rodrigo
Luciani, Aurelien
Madeira, Fabio
Marchler-Bauer, Aron
Mi, Huaiyu
Natale, Darren A.
Necci, Marco
Nuka, Gift
Orengo, Christine
Pandurangan, Arun P.
Paysan-Lafosse, Typhaine
Pesseat, Sebastien
Potter, Simon C.
Qureshi, Matloob A.
Rawlings, Neil D.
Redaschi, Nicole
Richardson, Lorna J.
Rivoire, Catherine
Salazar, Gustavo A.
Sangrador-Vegas, Amaia
Sigrist, Christian J. A.
Sillitoe, Ian
Sutton, Granger G.
Thanki, Narmada
Thomas, Paul D.
Tosatto, Silvio C. E.
Yong, Siew-Yit
Finn, Robert D.
[J]. NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) : D351 - D360

← 1 2 →