InterPro in 2022

被引：1209

作者：

Paysan-Lafosse, Typhaine ^{[1
]}

Blum, Matthias ^{[1
]}

Chuguransky, Sara ^{[1
]}

Grego, Tiago ^{[1
]}

Pinto, Beatriz Lazaro ^{[1
]}

Salazar, Gustavo A. ^{[1
]}

Bileschi, Maxwell L. ^{[2
]}

Bork, Peer ^{[3
,15
,16
]}

Bridge, Alan ^{[4
]}

Colwell, Lucy ^{[2
,5
]}

Gough, Julian ^{[6
]}

Haft, Daniel H. ^{[7
]}

Letunic, Ivica ^{[8
]}

Marchler-Bauer, Aron ^{[7
]}

Mi, Huaiyu ^{[9
]}

Natale, Darren A. ^{[10
]}

Orengo, Christine A. ^{[11
]}

Pandurangan, Arun P. ^{[6
,12
]}

Rivoire, Catherine ^{[4
]}

Sigrist, Christian J. A. ^{[4
]}

Sillitoe, Ian ^{[11
]}

Thanki, Narmada ^{[7
]}

Thomas, Paul D. ^{[9
]}

Tosatto, Silvio C. E. ^{[13
]}

Wu, Cathy H. ^{[10
,14
]}

Bateman, Alex ^{[1
]}

机构：

[1] European Mol Biol Lab, European Bioinformat Inst EMBL EBI, Wellcome Genome Campus, Hinxton CB10 1SD, Cambs, England

[2] Google Res, Brain Team, Cambridge, MA USA

[3] European Mol Biol Lab, Struct & Computat Biol Unit, Meyerhofstr 1, D-69117 Heidelberg, Germany

[4] CMU, Swiss Inst Bioinformat, Swiss Prot Grp, 1 Rue Michel Servet, CH-1211 Geneva 4, Switzerland

[5] Univ Cambridge, Dept Chem, Cambridge, England

[6] Cambridge Biomed Campus, MRC, Lab Mol Biol, Francis Crick Ave, Cambridge CB2 0QH, England

[7] Natl Ctr Biotechnol Informat, Natl Lib Med, NIH, 8600 Rockville Pike, Bethesda, MD 20894 USA

[8] Biobyte Solut GmbH, Bothestr 142, D-69126 Heidelberg, Germany

[9] Univ Southern Calif, Dept Prevent Med, Div Bioinformat, Los Angeles, CA 90033 USA

[10] Georgetown Univ, Prot Informat Resource, Med Ctr, Washington, DC 20007 USA

[11] UCL, Dept Struct & Mol Biol, Gower St, London WC1E 6BT, England

[12] Univ Cambridge, Dept Biochem, Sanger Bldg, Cambridge, England

[13] Univ Padua, Dept Biomed Sci, Via U Bassi 58-B, I-35131 Padua, Italy

[14] Univ Delaware, Ctr Bioinformat & Computat Biol & Prot Informat R, Newark, DE 19711 USA

[15] Yonsei Univ, Yonsei Frontier Lab YFL, Seoul 03722, South Korea

[16] Univ Wurzburg, Bioctr, Dept Bioinformat, D-97074 Wurzburg, Germany

来源：

NUCLEIC ACIDS RESEARCH | 2023年 / 51卷 / D1期

基金：

英国惠康基金; 英国生物技术与生命科学研究理事会; 美国国家科学基金会; 美国国家卫生研究院;

关键词：

FAMILY CLASSIFICATION; PROTEIN STRUCTURES; DATABASE; PREDICTION; TOPOLOGY;

D O I：

10.1093/nar/gkac993

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：

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (version 90.0) and its associated software, including updates to data content and to the website. These developments extend and enrich the information provided by InterPro, and provide a more user friendly access to the data. Additionally, we have worked on adding Pfam website features to the InterPro website, as the Pfam website will be retired in late 2022. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB. Moreover, we report the development of a card game as a method of engaging the non-scientific community. Finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction.

引用

页码：D418 / D427

页数：10

共 31 条

[1] The Structure-Function Linkage Database
Akiva, Eyal
Brown, Shoshana
Almonacid, Daniel E.
Barber, Alan E., II
Custer, Ashley F.
Hicks, Michael A.
Huang, Conrad C.
Lauck, Florian
Mashiyama, Susan T.
Meng, Elaine C.
Mischel, David
Morris, John H.
Ojha, Sunil
Schnoes, Alexandra M.
Stryke, Doug
Yunes, Jeffrey M.
Ferrin, Thomas E.
Holliday, Gemma L.
Babbitt, Patricia C.
[J]. NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) : D521 - D530
[2] The PRINTS database: a fine-grained protein sequence annotation and analysis resource-its status in 2012
Attwood, Teresa K.
Coletta, Alain
Muirhead, Gareth
Pavlopoulou, Athanasia
Philippou, Peter B.
Popov, Ivan
Roma-Mateo, Carlos
Theodosiou, Athina
Mitchell, Alex L.
[J]. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2012,
[3] Accurate prediction of protein structures and interactions using a three-track neural network
Baek, Minkyung
DiMaio, Frank
Anishchenko, Ivan
Dauparas, Justas
Ovchinnikov, Sergey
Lee, Gyu Rie
Wang, Jue
Cong, Qian
Kinch, Lisa N.
Schaeffer, R. Dustin
Millan, Claudia
Park, Hahnbeom
Adams, Carson
Glassman, Caleb R.
DeGiovanni, Andy
Pereira, Jose H.
Rodrigues, Andria V.
van Dijk, Alberdina A.
Ebrecht, Ana C.
Opperman, Diederik J.
Sagmeister, Theo
Buhlheller, Christoph
Pavkov-Keller, Tea
Rathinaswamy, Manoj K.
Dalwadi, Udit
Yip, Calvin K.
Burke, John E.
Garcia, K. Christopher
Grishin, Nick V.
Adams, Paul D.
Read, Randy J.
Baker, David
[J]. SCIENCE, 2021, 373 (6557) : 871 - +
[4] Using deep learning to annotate the protein universe
Bileschi, Maxwell L.
Belanger, David
Bryant, Drew
Sanderson, Theo
Carter, Brandon
Sculley, D.
Bateman, Alex
DePristo, Mark A.
Colwell, Lucy J.
[J]. NATURE BIOTECHNOLOGY, 2022, 40 (06) : 932 - +
[5] The InterPro protein families and domains database: 20 years on
Blum, Matthias
Chang, Hsin-Yu
Chuguransky, Sara
Grego, Tiago
Kandasaamy, Swaathi
Mitchell, Alex
Nuka, Gift
Paysan-Lafosse, Typhaine
Qureshi, Matloob
Raj, Shriya
Richardson, Lorna
Salazar, Gustavo A.
Williams, Lowri
Bork, Peer
Bridge, Alan
Gough, Julian
Haft, Daniel H.
Letunic, Ivica
Marchler-Bauer, Aron
Mi, Huaiyu
Natale, Darren A.
Necci, Marco
Orengo, Christine A.
Pandurangan, Arun P.
Rivoire, Catherine
Sigrist, Christian J. A.
Sillitoe, Ian
Thanki, Narmada
Thomas, Paul D.
Tosatto, Silvio C. E.
Wu, Cathy H.
Bateman, Alex
Finn, Robert D.
[J]. NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) : D344 - D354
[6] The Gene Ontology resource: enriching a GOld mine
Carbon, Seth
Douglass, Eric
Good, Benjamin M.
Unni, Deepak R.
Harris, Nomi L.
Mungall, Christopher J.
Basu, Siddartha
Chisholm, Rex L.
Dodson, Robert J.
Hartline, Eric
Fey, Petra
Thomas, Paul D.
Albou, Laurent-Philippe
Ebert, Dustin
Kesling, Michael J.
Mi, Huaiyu
Muruganujan, Anushya
Huang, Xiaosong
Mushayahama, Tremayne
LaBonte, Sandra A.
Siegele, Deborah A.
Antonazzo, Giulia
Attrill, Helen
Brown, Nick H.
Garapati, Phani
Marygold, Steven J.
Trovisco, Vitor
Dos Santos, Gil
Falls, Kathleen
Tabone, Christopher
Zhou, Pinglei
Goodman, Joshua L.
Strelets, Victor B.
Thurmond, Jim
Garmiri, Penelope
Ishtiaq, Rizwan
Rodriguez-Lopez, Milagros
Acencio, Marcio L.
Kuiper, Martin
Laegreid, Astrid
Logie, Colin
Lovering, Ruth C.
Kramarz, Barbara
Saverimuttu, Shirin C. C.
Pinheiro, Sandra M.
Gunn, Heather
Su, Renzhi
Thurlow, Katherine E.
Chibucos, Marcus
Giglio, Michelle
[J]. NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) : D325 - D334
[7] PIRSitePredict for protein functional site prediction using position-specific rules
Chen, Chuming
Wang, Qinghua
Huang, Hongzhan
Vinayaka, Cholanayakanahalli R.
Garavelli, John S.
Arighi, Cecilia N.
Natale, Darren A.
Wu, Cathy H.
[J]. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2019,
[8] AntiFam: a tool to help identify spurious ORFs in protein annotation
Eberhardt, Ruth Y.
Haft, Daniel H.
Punta, Marco
Martin, Maria
O'Donovan, Claire
Bateman, Alex
[J]. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2012,
[9] AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
Feldgarden, Michael
Brover, Vyacheslav
Gonzalez-Escalona, Narjol
Frye, Jonathan G.
Haendiges, Julie
Haft, Daniel H.
Hoffmann, Maria
Pettengill, James B.
Prasad, Arjun B.
Tillman, Glenn E.
Tyson, Gregory H.
Klimke, William
[J]. SCIENTIFIC REPORTS, 2021, 11 (01)
[10] Identification of all-against-all protein-protein interactions based on deep hash learning
Jiang, Yue
Wang, Yuxuan
Shen, Lin
Adjeroh, Donald A.
Liu, Zhidong
Lin, Jie
[J]. BMC BIOINFORMATICS, 2022, 23 (01)

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