default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDNucleic Acids Research, Volume 49
Volume 49, Number Database-Issue, January 2021
- Daniel J. Rigden
, Xosé M. Fernández:
The 2021 Nucleic Acids Research database issue and the online molecular biology database collection. D1-D9
Major Multi-Database Resources
- Eric W. Sayers, Jeffrey Beck, Evan Bolton, Devon Bourexis, James R. Brister, Kathi Canese, Donald C. Comeau, Kathryn Funk, Sunghwan Kim, William Klimke, Aron Marchler-Bauer, Melissa J. Landrum, Stacy Lathrop, Zhiyong Lu, Thomas L. Madden, Nuala A. O'Leary, Lon Phan, Sanjida H. Rangwala, Valerie A. Schneider, Yuri Skripchenko, Jiyao Wang, Jian Ye, Barton W. Trawick, Kim D. Pruitt, Stephen T. Sherry:
Database resources of the National Center for Biotechnology Information. D10-D17 - Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jing-Fa Xiao, Shunmin He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Shuhui Song, Lina Ma, Dong Zou, Dongmei Tian, Cuiping Li, Junwei Zhu, Zheng Gong, Meili Chen, Anke Wang, Yingke Ma, Mengwei Li, Xufei Teng, Ying Cui, Guangya Duan, Mochen Zhang, Tong Jin, Chengmin Shi, Zhenglin Du, Yadong Zhang, Chuandong Liu, Rujiao Li, Jingyao Zeng, Lili Hao, Shuai Jiang, Hua Chen, Dali Han, Tao Zhang, Wang Kang, Fei Yang, Jing Qu, Weiqi Zhang, Guanghui Liu, Lin Liu, Yang Zhang, Guangyi Niu, Tongtong Zhu, Changrui Feng, Xiaonan Liu, Yuansheng Zhang, Zhao Li, Ruru Chen, Qianpeng Li, Zhongyi Hua, Chao Jiang, Ziyuan Chen, Fangshu He, Yuyang Zhao, Yan Jin, Luqi Huang, Yuan Yuan, Chenfen Zhou, Qingwei Xu, Sheng He, Wei Ye, Ruifang Cao, Pengyu Wang, Yunchao Ling, Xing Yan, Qingzhong Wang, Qiang Du, Wenting Zong, Hongen Kang, Zhuang Xiong, Wendi Huan, Sirui Zhang, Qiguang Xia, Xiaojuan Fan, Zefeng Wang, Xu Chen, Tingting Chen, Sisi Zhang, Bixia Tang, Lili Dong, Zhewen Zhang, Zhonghuang Wang, Hailong Kang, Yanqing Wang, Song Wu, Ming Chen, Chang Liu, Yujia Xiong, Xueying Shao, Yanyan Li, Honghong Zhou, Xiaomin Chen, Yu Zheng, Quan Kang, Di Hao, Lili Zhang, Huaxia Luo, Yajing Hao, Peng Zhang, Zhi Nie, Shuhuan Yu, Jian Sang, Zhaohua Li, Xiangquan Zhang, Qing Zhou, Shuang Zhai, Yaping Zhang, Guodong Wang, Qianghui Zhu, Xin Li, Menghua Li, Jun Yan, Chen Li, Zhennan Wang, Xiangfeng Wang, Yuanming Liu, Hong Luo, Xiaoyuan Wu, Hai-Chun Jing, Lianhe Zhao, Jiajia Wang, Tinrui Song, Yi Zhao, Furrukh Mehmood, Shahid Ali, Amjad Ali, Shoaib Saleem, Irfan Hussain, Amir Ali Abbasi, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Yiran Tu, Yu Xue, Wanying Wu, Peifeng Ji, Fangqing Zhao, Xianwen Meng, Di Peng, Hao Luo, Feng Gao, Wanshan Ning, Shaofeng Lin, Teng Liu, An-Yuan Guo, Hao Yuan, Yong E. Zhang, Xiaodan Tan, Weizhi Zhang, Yubin Xie, Chenwei Wang, Chun-Jie Liu, De-Chang Yang, Feng Tian, Ge Gao, Dachao Tang, Lan Yao, Qinghua Cui, Ni A. An, Chuan-Yun Li, Xiaotong Luo:
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. D18-D28 - Gaia Cantelli, Guy Cochrane, Cath Brooksbank, Ellen M. McDonagh, Paul Flicek, Johanna R. McEntyre, Ewan Birney, Rolf Apweiler:
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. D29-D37
Nucleic Acid Sequence, Structure and Regulation
- Kyukwang Kim, Insu Jang, Mooyoung Kim, Jinhyuk Choi, Minseo Kim, Byungwook Lee, Inkyung Jung:
3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome. D38-D46 - Weiwei Jin, Qizhao Zhu, Yanbo Yang, Wenqian Yang, Dongyang Wang, Jiajun Yang, Xiaohui Niu, Debing Yu, Jing Gong:
Animal-APAdb: a comprehensive animal alternative polyadenylation database. D47-D54 - Fan Wang, Xuefeng Bai, Yuezhu Wang, Yong Jiang, Bo Ai, Yong Zhang, Yuejuan Liu, Mingcong Xu, Qiuyu Wang, Xiaole Han, Qi Pan, Yanyu Li, Xuecang Li, Jian Zhang, Jun Zhao, Guorui Zhang, Chenchen Feng, Jiang Zhu, Chunquan Li:
ATACdb: a comprehensive human chromatin accessibility database. D55-D64 - Yan Huang, Jing Wang, Yue Zhao, Huafeng Wang, Tianyuan Liu, Yuhe Li, Tianyu Cui, Weiyi Li, Yige Feng, Jiaxin Luo, Jiaqi Gong, Lin Ning, Yong Zhang, Dong Wang, Yang Zhang:
cncRNAdb: a manually curated resource of experimentally supported RNAs with both protein-coding and noncoding function. D65-D70 - Asami Fukuda, Yuichi Kodama, Jun Mashima, Takatomo Fujisawa, Osamu Ogasawara:
DDBJ update: streamlining submission and access of human data. D71-D75 - Almudena Ponce-Salvatierra, Pietro Boccaletto, Janusz M. Bujnicki:
DNAmoreDB, a database of DNAzymes. D76-D81 - Peter W. Harrison, Alisha Ahamed, Raheela Aslam, Blaise T. F. Alako, Josephine Burgin, Nicola Buso, Mélanie Courtot, Jun Fan, Dipayan Gupta, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Rodrigo Lopez, Simon Kay, Rasko Leinonen, Xin Liu, Colman O'Cathail, Amir Pakseresht, Young Mi Park, Stephane Pesant, Nadim Rahman, Jeena Rajan, Alexey Sokolov, Senthilnathan Vijayaraja, Zahra Waheed, Ahmad Zyoud, Tony Burdett, Guy Cochrane:
The European Nucleotide Archive in 2020. D82-D85 - Bailing Zhou, Baohua Ji, Kui Liu, Guodong Hu, Fei Wang, Qingshuai Chen, Ru Yu, Pingping Huang, Jing Ren, Chengang Guo, Huiying Zhao, Hongmei Zhang, Dongbo Zhao, Zhiwei Li, Qiangcheng Zeng, Jiafeng Yu, Yunqiang Bian, Zanxia Cao, Shicai Xu, Yuedong Yang, Yaoqi Zhou, Jihua Wang:
EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments. D86-D91 - Eric W. Sayers, Mark Cavanaugh, Karen Clark, Kim D. Pruitt, Conrad L. Schoch, Stephen T. Sherry, Ilene Karsch-Mizrachi:
GenBank. D92-D96 - Li Fang, Yunjin Li, Lu Ma, Qiyue Xu, Fei Tan, Geng Chen:
GRNdb: decoding the gene regulatory networks in diverse human and mouse conditions. D97-D103 - Semyon Kolmykov, Ivan S. Yevshin, Mikhail Kulyashov, Ruslan N. Sharipov, Yury V. Kondrakhin, Vsevolod J. Makeev, Ivan V. Kulakovskiy, Alexander E. Kel, Fedor A. Kolpakov:
GTRD: an integrated view of transcription regulation. D104-D111 - Kevin Rychel, Katherine Decker, Anand V. Sastry, Patrick V. Phaneuf, Saugat Poudel, Bernhard O. Palsson:
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. D112-D120 - Masanori Arita, Ilene Karsch-Mizrachi, Guy Cochrane:
The international nucleotide sequence database collaboration. D121-D124 - Peng Wang, Qiuyan Guo, Yangyang Hao, Qian Liu, Yue Gao, Hui Zhi, Xin Li, Shipeng Shang, Shuang Guo, Yunpeng Zhang, Shangwei Ning, Xia Li:
LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution. D125-D133 - Yujiao Tang, Kunqi Chen, Bowen Song, Jiongming Ma, Xiangyu Wu, Qingru Xu, Zhen Wei, Jionglong Su, Gang Liu, Rong Rong, Zhiliang Lu, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng:
m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome. D134-D143 - Zhidan Li, Yiming Zhang, Stephen J. Bush, Chao Tang, Li Chen, Dan Zhang, Araxi O. Urrutia, Jing-Wen Lin, Lu Chen:
MeDAS: a Metazoan Developmental Alternative Splicing database. D144-D150 - Nikos Perdikopanis, Georgios K. Georgakilas, Dimitris Grigoriadis, Vasileios Pierros, Ioannis Kavakiotis, Panagiotis Alexiou, Artemis G. Hatzigeorgiou:
DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs. D151-D159 - Lin Ning, Tianyu Cui, Boyang Zheng, Nuo Wang, Jiaxin Luo, Beilei Yang, Mengze Du, Jun Cheng, Yiying Dou, Dong Wang:
MNDR v3.0: mammal ncRNA-disease repository with increased coverage and annotation. D160-D164 - Lianhe Zhao, Jiajia Wang, Yanyan Li, Tingrui Song, Yang Wu, Shuangsang Fang, Dechao Bu, Hui Li, Liang Sun, Dong Pei, Yu Zheng, Jianqin Huang, Mingqing Xu, Runsheng Chen, Yi Zhao, Shunmin He:
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. D165-D171 - Vinícius G. Contessoto, Ryan R. Cheng, Arya Hajitaheri, Esteban Dodero-Rojas, Matheus F. Mello, Erez Lieberman Aiden, Peter G. Wolynes, Michele Di Pierro, José N. Onuchic:
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome. D172-D182 - Pan Li, Xiaolin Zhou, Kui Xu, Qiangfeng Cliff Zhang:
RASP: an atlas of transcriptome-wide RNA secondary structure probing data. D183-D191 - Ioanna Kalvari, Eric P. Nawrocki, Nancy Ontiveros-Palacios, Joanna Argasinska, Kevin Lamkiewicz, Manja Marz, Sam Griffiths-Jones, Claire Toffano-Nioche, Daniel Gautheret, Zasha Weinberg, Elena Rivas, Sean R. Eddy, Robert D. Finn, Alex Bateman, Anton I. Petrov:
Rfam 14: expanded coverage of metagenomic, viral and microRNA families. D192-D200 - Qin Li, Hongyan Lai, Yuchen Li, Bing Chen, Siyuan Chen, Yan Li, Zhaohui Huang, Zhiqiang Meng, Peng Wang, Zhixiang Hu, Shenglin Huang:
RJunBase: a database of RNA splice junctions in human normal and cancerous tissues. D201-D211 - Blake A. Sweeney, Anton I. Petrov, Carlos Eduardo Ribas, Robert D. Finn, Alex Bateman, Maciej Szymanski, Wojciech M. Karlowski, Stefan E. Seemann, Jan Gorodkin, Jamie J. Cannone, Robin Ray Gutell, Simon Kay, Steven J. Marygold, Gilberto dos Santos, Adam Frankish, Jonathan M. Mudge, Ruth Barshir, Simon Fishilevich, Patricia P. Chan, Todd M. Lowe, Ruth L. Seal, Elspeth A. Bruford, Simona Panni, Pablo Porras, Dimitra Karagkouni, Artemis G. Hatzigeorgiou, Lina Ma, Zhang Zhang, Pieter-Jan Volders, Pieter Mestdagh, Sam Griffiths-Jones, Bastian Fromm, Kevin J. Peterson, Ioanna Kalvari, Eric P. Nawrocki, Anton S. Petrov, Shuai Weng, Philia Bouchard-Bourelle, Michelle S. Scott, Lauren M. Lui, David Hoksza, Ruth C. Lovering, Barbara Kramarz, Prita Mani, Sridhar Ramachandran, Zasha Weinberg:
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. D212-D220 - Wanwen Zeng, Shengquan Chen, Xuejian Cui, Xiaoyang Chen, Zijing Gao, Rui Jiang:
SilencerDB: a comprehensive database of silencers. D221-D228 - Jorge A. Marchand, Merrick D. Pierson smela, Thomas H. H. Jordan, Kamesh Narasimhan, George M. Church:
TBDB: a database of structurally annotated T-box riboswitch: tRNA pairs. D229-D235 - Wendi Huang, Yunchao Ling, Sirui Zhang, Qiguang Xia, Ruifang Cao, Xiaojuan Fan, Zhaoyuan Fang, Zefeng Wang, Guoqing Zhang:
TransCirc: an interactive database for translatable circular RNAs based on multi-omics evidence. D236-D242 - Federico Marini, Denise Scherzinger, Sven Danckwardt:
TREND-DB - a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation. D243-D253 - Ningshan Li, Nayang Shan, Lingeng Lu, Zuoheng Wang:
tRFtarget: a database for transfer RNA-derived fragment targets. D254-D260
Protein Sequence and Structure, Motifs and Domains
- Vinay Ayyappan, Ricky Wat, Calvin Barber, Christina A. Vivelo, Kathryn Gauch, Pat Visanpattanasin, Garth Cook, Christos Sazeides, Anthony Kar Lun Leung:
ADPriboDB 2.0: an updated database of ADP-ribosylated proteins. D261-D265 - Ian Sillitoe, Nicola Bordin, Natalie L. Dawson, Vaishali P. Waman, Paul Ashford, Harry M. Scholes, Camilla S. M. Pang, Laurel Woodridge, Clemens Rauer, Neeladri Sen, Mahnaz Abbasian, Sean Le Cornu, Su Datt Lam, Karel Berka, Ivana Hutarová Vareková, Radka Svobodová Vareková, Jonathan G. Lees, Christine A. Orengo:
CATH: increased structural coverage of functional space. D266-D273 - Michael Y. Galperin, Yuri I. Wolf, Kira S. Makarova, Roberto Vera Alvarez, David Landsman, Eugene V. Koonin:
COG database update: focus on microbial diversity, model organisms, and widespread pathogens. D274-D281 - Ragul Gowthaman, Johnathan D. Guest, Rui Yin, Jared Adolf-Bryfogle, William R. Schief, Brian G. Pierce:
CoV3D: a database of high resolution coronavirus protein structures. D282-D287 - Malak Pirtskhalava, Anthony A. Amstrong, Maia Grigolava, Mindia Chubinidze, Evgenia Alimbarashvili, Boris Vishnepolsky, Andrei E. Gabrielian, Alex Rosenthal, Darrell E. Hurt, Michael Tartakovsky:
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics. D288-D297 - Bi Zhao, Akila Katuwawala, Christopher J. Oldfield, A. Keith Dunker, Eshel Faraggi, Jörg Gsponer, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Zoran Obradovic, Johannes Söding, Martin Steinegger, Yaoqi Zhou, Lukasz A. Kurgan:
DescribePROT: database of amino acid-level protein structure and function predictions. D298-D308 - Zakaria Louadi, Kevin Yuan, Alexander Greß, Olga Tsoy, Olga V. Kalinina, Jan Baumbach, Tim Kacprowski, Markus List:
DIGGER: exploring the functional role of alternative splicing in protein interactions. D309-D318 - Jan Stourac, Juraj Dubrava, Milos Musil, Jana Horackova, Jirí Damborský, Stanislav Mazurenko, David Bednar:
FireProtDB: database of manually curated protein stability data. D319-D324 - Seth Carbon, Eric Douglass, Benjamin M. Good, Deepak R. Unni, Nomi L. Harris, Christopher J. Mungall, Siddartha Basu, Rex L. Chisholm, Robert J. Dodson, Eric Hartline, Petra Fey, Paul D. Thomas, Laurent-Philippe Albou, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte, Deborah A. Siegele, Giulia Antonazzo, Helen Attrill, Nick H. Brown, Phani V. Garapati, Steven J. Marygold, Vitor Trovisco, Gilberto dos Santos, Kathleen Falls, Christopher J. Tabone, Pinglei Zhou, Joshua L. Goodman, Victor B. Strelets, Jim Thurmond, Penelope Garmiri, Rizwan Ishtiaq, Milagros Rodríguez-López, Marcio Luis Acencio, Martin Kuiper, Astrid Lægreid, Colin Logie, Ruth C. Lovering, Barbara Kramarz, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow, Marcus C. Chibucos, Michelle G. Giglio, Suvarna Nadendla, James B. Munro, Rebecca C. Jackson, Margaret J. Duesbury, Noemi del-Toro, Birgit H. M. Meldal, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras, Sandra E. Orchard, Anjali Shrivastava, Hsin-Yu Chang, Robert D. Finn, Alex L. Mitchell, Neil D. Rawlings, Lorna J. Richardson, Amaia Sangrador-Vegas, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford, Valerie Wood, Jaqueline Hayles, Jürg Bähler, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Cody Plasterer, Marek Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry, Stacia R. Engel, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann, Pascale Gaudet, Anne Morgat, Erica Bakker, Tanya Z. Berardini, Leonore Reiser, Shabari Subramaniam, Eva Huala, Cecilia N. Arighi, Andrea H. Auchincloss, Kristian B. Axelsen, Ghislaine Argoud-Puy, Alex Bateman, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler, Lionel Breuza, Alan J. Bridge, Ramona Britto, Hema Bye-A-Jee, Cristina Casals-Casas, Elisabeth Coudert, Paul Denny, Anne Estreicher, Maria Livia Famiglietti, George E. Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko, Florence Jungo, Kati Laiho, Philippe Le Mercier, Damien Lieberherr, Antonia Lock, Yvonne Lussi, Alistair MacDougall, Michele Magrane, Maria Jesus Martin, Patrick Masson, Darren A. Natale, Nevila Hyka-Nouspikel, Ivo Pedruzzi, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire, Elena Speretta, Shyamala Sundaram, Nidhi Tyagi, Kate Warner, Rossana Zaru, Cathy H. Wu, Alexander D. Diehl, Juancarlos Chan, Christian A. Grove, Raymond Y. N. Lee, Hans-Michael Müller, Daniela Raciti, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin L. Howe, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper, Justin Elser:
The Gene Ontology resource: enriching a GOld mine. D325-D334 - Albert J. Kooistra, Stefan Mordalski, Gáspár Pándy-Szekeres, Mauricio Esguerra, Alibek Mamyrbekov, Christian Munk, György M. Keserü, David E. Gloriam:
GPCRdb in 2021: integrating GPCR sequence, structure and function. D335-D343 - Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasamy, Alex L. Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna J. Richardson, Gustavo A. Salazar, Lowri Williams, Peer Bork, Alan J. Bridge, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Marco Necci, Christine A. Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman, Robert D. Finn:
The InterPro protein families and domains database: 20 years on. D344-D354 - Georgina Csizmadia, Gábor Erdös, Hedvig Tordai, Rita Padányi, Silvio C. E. Tosatto, Zsuzsanna Dosztányi, Tamás Hegedüs:
The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes. D355-D360 - Damiano Piovesan, Marco Necci, Nahuel Escobedo, Alexander Miguel Monzon, András Hatos, Ivan Micetic, Federica Quaglia, Lisanna Paladin, Pathmanaban Ramasamy, Zsuzsanna Dosztányi, Wim F. Vranken, Norman E. Davey, Gustavo D. Parisi, Mónika Fuxreiter, Silvio C. E. Tosatto:
MobiDB: intrinsically disordered proteins in 2021. D361-D367 - Chang Chen, Haipeng Liu, Shadi Zabad, Nina Rivera, Emily Rowin, Maheen Hassan, Stephanie M. Gomez de Jesus, Paola S. Llinás santos, Karyna Kravchenko, Mariia Mikhova, Sophia Ketterer, Annabel Shen, Sophia Shen, Erin Navas, Bryan Horan, Jaak Raudsepp, Constance J. Jeffery:
MoonProt 3.0: an update of the moonlighting proteins database. D368-D372 - Adrian M. Altenhoff, Clément-Marie Train, Kimberly J. Gilbert, Ishita Mediratta, Tarcisio Mendes de Farias, David Moi, Yannis Nevers, Hale-Seda Radoykova, Victor Rossier, Alex Warwick Vesztrocy, Natasha M. Glover, Christophe Dessimoz:
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. D373-D379 - Marie A. Brunet, Jean-François Lucier, Maxime Levesque, Sébastien Leblanc, Jean-Francois Jacques, Hassan R. H. Al-Saedi, Noé Guilloy, Frédéric Grenier, Mariano Avino, Isabelle Fournier, Michel Salzet, Aïda Ouangraoua, Michelle S. Scott, François-Michel Boisvert, Xavier Roucou:
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. D380-D388 - Evgeny M. Zdobnov, Dmitry Kuznetsov, Fredrik Tegenfeldt, Mosè Manni, Matthew Berkeley, Evgenia V. Kriventseva:
OrthoDB in 2020: evolutionary and functional annotations of orthologs. D389-D393 - Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayahama, Paul D. Thomas:
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. D394-D411 - Jaina Mistry, Sara Chuguransky, Lowri Williams, Matloob Qureshi, Gustavo A. Salazar, Erik L. L. Sonnhammer, Silvio C. E. Tosatto, Lisanna Paladin, Shriya Raj, Lorna J. Richardson, Robert D. Finn, Alex Bateman:
Pfam: The protein families database in 2021. D412-D419 - Rahul Nikam, A. Kulandaisamy, K. Harini, Divya Sharma, M. Michael Gromiha:
ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years. D420-D424 - Maiwen Caudron-Herger, Ralf E. Jansen, Elsa Wassmer, Sven Diederichs:
RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions. D425-D436 - Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V. Crichlow, Cole H. Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sai Ganesan, David S. Goodsell, Sutapa Ghosh, Rachel Kramer Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Persikova, Christopher Randle, Alexander S. Rose, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Yi-Ping Tao, Maria Voigt, John D. Westbrook, Jasmine Young, Christine Zardecki, Marina Zhuravleva:
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. D437-D451 - Lisanna Paladin, Martina Bevilacqua, Sara Errigo, Damiano Piovesan, Ivan Micetic, Marco Necci, Alexander Miguel Monzon, Maria Laura Fabre, José Luis López, Juliet F. Nilsson, Javier Ríos, Pablo Lorenzano Menna, Maia Cabrera, Martin Gonzalez Buitron, Mariane Gonçalves Kulik, Sebastian Fernandez Alberti, María Silvina Fornasari, Gustavo D. Parisi, Antonio Lagares, Layla Hirsh, Miguel A. Andrade-Navarro, Andrey V. Kajava, Silvio C. E. Tosatto:
RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures. D452-D457 - Ivica Letunic, Supriya Khedkar, Peer Bork:
SMART: recent updates, new developments and status in 2020. D458-D460 - Milton H. Saier Jr., Vamsee S. Reddy, Gabriel Moreno-Hagelsieb, Kevin J. Hendargo, Yichi Zhang, Vasu Iddamsetty, Katie Jing Kay Lam, Nuo Tian, Steven Russum, Jianing Wang, Arturo Medrano-Soto:
The Transporter Classification Database (TCDB): 2021 update. D461-D467 - Si-Yi Chen, Tao Yue, Qian Lei, An-Yuan Guo:
TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function. D468-D474 - Joicymara S. Xavier, Thanh-Binh Nguyen, Malancha Karmarkar, Stephanie Portelli, Pâmela M. Rezende, João P. L. Velloso, David B. Ascher, Douglas E. V. Pires:
ThermoMutDB: a thermodynamic database for missense mutations. D475-D479 - Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee, Ray Coetzee, Austra Cukura, Alan W. Sousa da Silva, Paul Denny, Tunca Dogan, Thankgod Ebenezer, Jun Fan, Leyla Jael García Castro, Penelope Garmiri, George E. Georghiou, Leonardo Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Petteri Jokinen, Vishal Joshi, Dushyanth Jyothi, Antonia Lock, Rodrigo Lopez, Aurelien Luciani, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Manuela Menchi, Alok Mishra, Katie Moulang, Andrew Nightingale, Carla Susana Oliveira, Sangya Pundir, Guoying Qi, Shriya Raj, Daniel Rice, Milagros Rodríguez-López, Rabie Saidi, Joseph Sampson, Tony Sawford, Elena Speretta, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Vladimir Volynkin, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Alan J. Bridge, Sylvain Poux, Nicole Redaschi, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Edouard De Castro, Kamal Chikh Echioukh, Elisabeth Coudert, Béatrice A. Cuche, Mikael Doche, Dolnide Dornevil, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Sebastien Gehant, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Guillaume Keller, Arnaud Kerhornou, Vicente Lara, Philippe Le Mercier, Damien Lieberherr, Thierry Lombardot, Xavier Martin, Patrick Masson, Anne Morgat, Teresa Batista Neto, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Monica Pozzato, Manuela Pruess, Catherine Rivoire, Christian J. A. Sigrist, Karin Sonesson, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Laure Verbregue, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, John S. Garavelli, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Lai-Su Yeh, Jian Zhang, Patrick Ruch, Douglas Teodoro:
UniProt: the universal protein knowledgebase in 2021. D480-D489
Metabolic and Signalling Pathways, Enzymes
- Satria A. Kautsar, Kai Blin, Simon Shaw, Tilmann Weber, Marnix H. Medema:
BiG-FAM: the biosynthetic gene cluster families database. D490-D497 - Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg:
BRENDA, the ELIXIR core data resource in 2021: new developments and updates. D498-D508 - Chuanyu Lyu, Tong Chen, Bo Qiang, Ningfeng Liu, Heyu Wang, Liangren Zhang, Zhenming Liu:
CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean. D509-D515 - Yosef D. Roth, Zhouyang Lian, Saahith Pochiraju, Bilal Shaikh, Jonathan R. Karr:
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. D516-D522 - Catherine Ausland, Jinfang Zheng, Haidong Yi, Bowen Yang, Tang Li, Xuehuan Feng, Bo Zheng, Yanbin Yin:
dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates. D523-D528 - Matthew E. Berginski, Nienke Moret, Changchang Liu, Dennis Goldfarb, Peter K. Sorger, Shawn M. Gomez:
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. D529-D535 - Shu Tadaka, Eiji Hishinuma, Shohei Komaki, Ikuko N. Motoike, Junko Kawashima, Daisuke Saigusa, Jin Inoue, Jun Takayama, Yasunobu Okamura, Yuichi Aoki, Matsuyuki Shirota, Akihito Otsuki, Fumiki Katsuoka, Atsushi Shimizu, Gen Tamiya, Seizo Koshiba, Makoto Sasaki, Masayuki Yamamoto, Kengo Kinoshita:
jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese population. D536-D544 - Minoru Kanehisa, Miho Furumichi, Yoko Sato, Mari Ishiguro-Watanabe, Mao Tanabe:
KEGG: integrating viruses and cellular organisms. D545-D551 - Ruifeng Hu, Hao-Dong Xu, Peilin Jia, Zhongming Zhao:
KinaseMD: kinase mutations and drug response database. D552-D561 - Georgi K. Kanev, Chris de Graaf, Bart A. Westerman, Iwan J. P. de Esch, Albert J. Kooistra:
KLIFS: an overhaul after the first 5 years of supporting kinase research. D562-D569 - Sébastien Moretti, T. Van Du Tran, Florence Mehl, Mark Ibberson, Marco Pagni:
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. D570-D574 - Samuel M. D. Seaver, Filipe Liu, Qizhi Zhang, James G. Jeffryes, José P. Faria, Janaka N. Edirisinghe, Michael B. Mundy, Nicholas Chia, Elad Noor, Moritz Emanuel Beber, Aaron A. Best, Matthew DeJongh, Jeffrey A. Kimbrel, Patrik D'haeseleer, Sean R. McCorkle, Jay R. Bolton, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin, Christopher S. Henry:
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. D575-D588 - Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Do Hai Dang, James J. Cimino, Jake Y. Chen:
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies. D589-D599 - Aurélien F. A. Moumbock, Mingjie Gao, Ammar Qaseem, Jianyu Li, Pascal A. Kirchner, Bakoh Ndingkokhar, Boris D. Bekono, Conrad Veranso Simoben, Smith B. Babiaka, Yvette I. Malange, Florian Sauter, Paul F. Zierep, Fidele Ntie-Kang, Stefan Günther:
StreptomeDB 3.0: an updated compendium of streptomycetes natural products. D600-D604 - Damian Szklarczyk, Annika L. Gable, Katerina C. Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T. Doncheva, Marc Legeay, Tao Fang, Peer Bork, Lars Juhl Jensen, Christian von Mering:
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. D605-D612 - Marvin Martens, Ammar Ammar, Anders Riutta, Andra Waagmeester, Denise N. Slenter, Kristina Hanspers, Ryan A. Miller, Daniela Digles, Elisson N. Lopes, Friederike Ehrhart, Lauren J. Dupuis, Laurent A. Winckers, Susan L. Coort, Egon L. Willighagen, Chris T. A. Evelo, Alexander R. Pico, Martina Kutmon:
WikiPathways: connecting communities. D613-D621
Viruses, Bacteria and Fungi
- Le Huang, Bowen Yang, Haidong Yi, Amina Asif, Jiawei Wang, Trevor Lithgow, Han Zhang, Fayyaz ul Amir Afsar Minhas, Yanbin Yin:
AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses. D622-D629 - Jiawei Wang, Wei Dai, Jiahui Li, Qi Li, Ruopeng Xie, Yanju Zhang, Christopher Stubenrauch, Trevor Lithgow:
AcrHub: an integrative hub for investigating, predicting and mapping anti-CRISPR proteins. D630-D638 - Kai Blin, Simon Shaw, Satria A. Kautsar, Marnix H. Medema, Tilmann Weber:
The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes. D639-D643 - Ye Feng, Shengmei Zou, Hangfei Chen, Yunsong Yu, Zhi Ruan:
BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking. D644-D650 - Jiawei Wang, Jiahui Li, Yi Hou, Wei Dai, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Tieli Zhou, Von Torres, Iain Hay, Christopher Stubenrauch, Yanju Zhang, Jiangning Song, Trevor Lithgow:
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. D651-D659 - Rafael Mamede, Pedro Vila-Cerqueira, Mickael Silva, João A. Carriço, Mário Ramirez:
Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas. D660-D666