Database Commons a catalog of biological databases

Database Commons - UniProt

UniProt

Citations: 13605

z-index 835.74

Short name UniProt
Full name The Universal Protein Resource
Description UniProt provides the scientific community with a comprehensive,high-quality and freely accessible resource of protein sequence and functional information.
URL http://www.uniprot.org/
Year founded 2002
Last update & version 2017-02-15    2017_02
Availability Free to all users
University/Institution hosted European Bioinformatics Institute
Address Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
City Cambridge
Province/State Cambridgeshire
Country/Region United Kingdom
Contact name The UniProt Consortium
Contact email agb@ebi.ac.uk
Data type(s)
Major organism(s)
Keyword(s)
  • protein sequence
  • protein structure
Publication(s)
  • UniProt: the universal protein knowledgebase. [PMID: 27899622]

    Nucleic acids research 2017:45(D1)
    1 Citations (Google Scholar as of 2017-03-29)

    Abstract: The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, of which over half a million sequences have been curated by experts who critically review experimental and predicted data for each protein. The remainder are automatically annotated based on rule systems that rely on the expert curated knowledge. Since our last update in 2014, we have more than doubled the number of reference proteomes to 5631, giving a greater coverage of taxonomic diversity. We implemented a pipeline to remove redundant highly similar proteomes that were causing excessive redundancy in UniProt. The initial run of this pipeline reduced the number of sequences in UniProt by 47 million. For our users interested in the accessory proteomes, we have made available sets of pan proteome sequences that cover the diversity of sequences for each species that is found in its strains and sub-strains. To help interpretation of genomic variants, we provide tracks of detailed protein information for the major genome browsers. We provide a SPARQL endpoint that allows complex queries of the more than 22 billion triples of data in UniProt (http://sparql.uniprot.org/). UniProt resources can be accessed via the website at http://www.uniprot.org/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • Minimizing proteome redundancy in the UniProt Knowledgebase. [PMID: 28025334]

    Borisas Bursteinas, Ramona Britto, Benoit Bely, Andrea Auchincloss, Catherine Rivoire, Nicole Redaschi, Claire O'Donovan, Maria Jesus Martin
    Database : the journal of biological databases and curation 2016:2016
    0 Citations (Google Scholar as of 2017-03-29)

    Abstract: Advances in high-throughput sequencing have led to an unprecedented growth in genome sequences being submitted to biological databases. In particular, the sequencing of large numbers of nearly identical bacterial genomes during infection outbreaks and for other large-scale studies has resulted in a high level of redundancy in nucleotide databases and consequently in the UniProt Knowledgebase (UniProtKB). Redundancy negatively impacts on database searches by causing slower searches, an increase in statistical bias and cumbersome result analysis. The redundancy combined with the large data volume increases the computational costs for most reuses of UniProtKB data. All of this poses challenges for effective discovery in this wealth of data. With the continuing development of sequencing technologies, it is clear that finding ways to minimize redundancy is crucial to maintaining UniProt's essential contribution to data interpretation by our users. We have developed a methodology to identify and remove highly redundant proteomes from UniProtKB. The procedure identifies redundant proteomes by performing pairwise alignments of sets of sequences for pairs of proteomes and subsequently, applies graph theory to find dominating sets that provide a set of non-redundant proteomes with a minimal loss of information. This method was implemented for bacteria in mid-2015, resulting in a removal of 50 million proteins in UniProtKB. With every new release, this procedure is used to filter new incoming proteomes, resulting in a more scalable and scientifically valuable growth of UniProtKB.Database URL: http://www.uniprot.org/proteomes/. © The Author(s) 2016. Published by Oxford University Press.

  • UniProt: a hub for protein information. [PMID: 25348405]

    Nucleic acids research 2015:43(Database issue)
    1268 Citations (Google Scholar as of 2017-03-29)

    Abstract: UniProt is an important collection of protein sequences and their annotations, which has doubled in size to 80 million sequences during the past year. This growth in sequences has prompted an extension of UniProt accession number space from 6 to 10 characters. An increasing fraction of new sequences are identical to a sequence that already exists in the database with the majority of sequences coming from genome sequencing projects. We have created a new proteome identifier that uniquely identifies a particular assembly of a species and strain or subspecies to help users track the provenance of sequences. We present a new website that has been designed using a user-experience design process. We have introduced an annotation score for all entries in UniProt to represent the relative amount of knowledge known about each protein. These scores will be helpful in identifying which proteins are the best characterized and most informative for comparative analysis. All UniProt data is provided freely and is available on the web at http://www.uniprot.org/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • Activities at the Universal Protein Resource (UniProt). [PMID: 24253303]

    Nucleic acids research 2014:42(Database issue)
    848 Citations (Google Scholar as of 2017-03-29)

    Abstract: The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequences and functional annotation. It integrates, interprets and standardizes data from literature and numerous resources to achieve the most comprehensive catalog possible of protein information. The central activities are the biocuration of the UniProt Knowledgebase and the dissemination of these data through our Web site and web services. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.

  • Update on activities at the Universal Protein Resource (UniProt) in 2013. [PMID: 23161681]

    Nucleic acids research 2013:41(Database issue)
    83 Citations (Google Scholar as of 2016-04-29)

    Abstract: The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase. It integrates, interprets and standardizes data from numerous resources to achieve the most comprehensive catalogue of protein sequences and functional annotation. UniProt comprises four major components, each optimized for different uses, the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.

  • Reorganizing the protein space at the Universal Protein Resource (UniProt). [PMID: 22102590]

    Nucleic acids research 2012:40(Database issue)
    1430 Citations (Google Scholar as of 2017-03-29)

    Abstract: The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. A key development at UniProt is the provision of complete, reference and representative proteomes. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org.

  • UniProt Knowledgebase: a hub of integrated protein data. [PMID: 21447597]

    Michele Magrane, null null
    Database : the journal of biological databases and curation 2011:2011
    1012 Citations (Google Scholar as of 2017-03-29)

    Abstract: The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing a unified view of protein sequence and functional information. Manual and automatic annotation procedures are used to add data directly to the database while extensive cross-referencing to more than 120 external databases provides access to additional relevant information in more specialized data collections. UniProtKB also integrates a range of data from other resources. All information is attributed to its original source, allowing users to trace the provenance of all data. The UniProt Consortium is committed to using and promoting common data exchange formats and technologies, and UniProtKB data is made freely available in a range of formats to facilitate integration with other databases. Database URL: http://www.uniprot.org/

  • The Universal Protein Resource (UniProt) in 2010. [PMID: 19843607]

    Nucleic acids research 2010:38(Database issue)
    705 Citations (Google Scholar as of 2017-03-29)

    Abstract: The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is updated and distributed every 3 weeks and can be accessed online for searches or download at http://www.uniprot.org.

  • The Universal Protein Resource (UniProt) 2009. [PMID: 18836194]

    Nucleic acids research 2009:37(Database issue)
    1307 Citations (Google Scholar as of 2016-03-31)

    Abstract: The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information that is essential for modern biological research. UniProt is produced by the UniProt Consortium which consists of groups from the European Bioinformatics Institute, the Protein Information Resource and the Swiss Institute of Bioinformatics. The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, a user-friendly UniProt website and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. One of the key achievements of the UniProt consortium in 2008 is the completion of the first draft of the complete human proteome in UniProtKB/Swiss-Prot. This manually annotated representation of all currently known human protein-coding genes was made available in UniProt release 14.0 with 20 325 entries. UniProt is updated and distributed every three weeks and can be accessed online for searches or downloaded at www.uniprot.org.

  • The universal protein resource (UniProt). [PMID: 18045787]

    Nucleic acids research 2008:36(Database issue)
    1424 Citations (Google Scholar as of 2017-03-29)

    Abstract: The Universal Protein Resource (UniProt) provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation. The UniProt Consortium is a collaboration between the European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB). The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt website, and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of four major components, each optimized for different uses: the UniProt Knowledgebase, the UniProt Reference Clusters, the UniProt Archive and the UniProt Metagenomic and Environmental Sequences database. UniProt is updated and distributed every three weeks, and can be accessed online for searches or download at http://www.uniprot.org.

  • The Universal Protein Resource (UniProt). [PMID: 17142230]

    Nucleic acids research 2007:35(Database issue)
    1306 Citations (Google Scholar as of 2016-03-31)

    Abstract: The ability to store and interconnect all available information on proteins is crucial to modern biological research. Accordingly, the Universal Protein Resource (UniProt) plays an increasingly important role by providing a stable, comprehensive, freely accessible central resource on protein sequences and functional annotation. UniProt is produced by the UniProt Consortium, formed in 2002 by the European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB). The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt web site and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of three major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase and the UniProt Reference Clusters. An additional component consisting of metagenomic and environmental sequences has recently been added to UniProt to ensure availability of such sequences in a timely fashion. UniProt is updated and distributed on a bi-weekly basis and can be accessed online for searches or download at http://www.uniprot.org.

  • The Universal Protein Resource (UniProt): an expanding universe of protein information. [PMID: 16381842]

    Cathy H Wu, Rolf Apweiler, Amos Bairoch, Darren A Natale, Winona C Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria J Martin, Raja Mazumder, Claire O'Donovan, Nicole Redaschi, Baris Suzek
    Nucleic acids research 2006:34(Database issue)
    943 Citations (Google Scholar as of 2017-03-29)

    Abstract: The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/.

  • The Universal Protein Resource (UniProt). [PMID: 15608167]

    Amos Bairoch, Rolf Apweiler, Cathy H Wu, Winona C Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria J Martin, Darren A Natale, Claire O'Donovan, Nicole Redaschi, Lai-Su L Yeh
    Nucleic acids research 2005:33(Database issue)
    1640 Citations (Google Scholar as of 2017-03-29)

    Abstract: The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the Swiss-Prot, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/Swiss-Prot, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two weeks.

  • UniProt: the Universal Protein knowledgebase. [PMID: 14681372]

    Rolf Apweiler, Amos Bairoch, Cathy H Wu, Winona C Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria J Martin, Darren A Natale, Claire O'Donovan, Nicole Redaschi, Lai-Su L Yeh
    Nucleic acids research 2004:32(Database issue)
    1638 Citations (Google Scholar as of 2017-03-29)

    Abstract: To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar Swiss-Prot (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt.

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Accessibility

Rate of accessibility:
HTTP status codeDate requested
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200 OK2018-04-13
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200 OK2018-02-27
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200 OK2018-02-13
200 OK2018-02-09
200 OK2018-02-06
200 OK2018-02-02
200 OK2018-01-30
200 OK2018-01-26
200 OK2018-01-23
200 OK2018-01-19
200 OK2018-01-16
200 OK2018-01-12
200 OK2018-01-09
200 OK2018-01-05
200 OK2018-01-02
200 OK2017-12-29
200 OK2017-12-26
200 OK2017-12-22
200 OK2017-12-19
200 OK2017-12-15
200 OK2017-12-12
200 OK2017-12-08
200 OK2017-12-05
200 OK2017-12-01
200 OK2017-11-28
200 OK2017-11-24
200 OK2017-11-21
200 OK2017-11-17
200 OK2017-11-14
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200 OK2017-11-07
200 OK2017-11-03
200 OK2017-10-31
200 OK2017-10-27
200 OK2017-10-24
200 OK2017-10-20
-1 Failed2017-10-17
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200 OK2017-10-10
200 OK2017-10-06
200 OK2017-10-03
200 OK2017-09-29
200 OK2017-09-26
200 OK2017-09-22
200 OK2017-09-19
200 OK2017-09-15
200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
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200 OK2017-02-28
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200 OK2017-02-17
200 OK2017-02-14
200 OK2017-02-10
200 OK2017-02-07
200 OK2017-02-03
200 OK2017-01-31
200 OK2017-01-27
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200 OK2017-01-03
200 OK2016-12-30
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200 OK2016-12-23
200 OK2016-12-20
200 OK2016-12-16
200 OK2016-12-13
200 OK2016-12-09
200 OK2016-12-06
200 OK2016-12-02
200 OK2016-11-29
200 OK2016-11-25
200 OK2016-11-22
-1 Failed2016-11-18
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200 OK2016-11-08
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200 OK2016-11-01
200 OK2016-10-28
200 OK2016-10-25
200 OK2016-10-21
200 OK2016-10-18
200 OK2016-10-14
200 OK2016-10-11
200 OK2016-10-07
200 OK2016-10-04
200 OK2016-09-30
200 OK2016-09-27
200 OK2016-09-23
200 OK2016-09-20
200 OK2016-09-16
200 OK2016-09-13
200 OK2016-09-09
200 OK2016-09-06
200 OK2016-09-02
200 OK2016-08-30
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200 OK2016-08-16
200 OK2016-08-12
200 OK2016-08-09
200 OK2016-08-05
200 OK2016-08-02
200 OK2016-07-29
200 OK2016-07-26
200 OK2016-07-22
200 OK2016-07-19
200 OK2016-07-15
200 OK2016-07-12
200 OK2016-07-08
200 OK2016-07-05
200 OK2016-07-01
200 OK2016-06-28
200 OK2016-06-24
200 OK2016-06-21
200 OK2016-06-17
200 OK2016-06-14
200 OK2016-06-10
200 OK2016-06-07
200 OK2016-06-03
200 OK2016-05-31
200 OK2016-05-27
200 OK2016-05-24
200 OK2016-05-20
200 OK2016-05-17
200 OK2016-05-13
200 OK2016-05-10
200 OK2016-05-06
200 OK2016-05-03
200 OK2016-04-29
200 OK2016-04-26
200 OK2016-04-22
200 OK2016-04-19
200 OK2016-04-15
200 OK2016-04-12
200 OK2016-04-08
200 OK2016-04-05
200 OK2016-04-01
200 OK2016-03-29
200 OK2016-03-28
200 OK2016-03-25
200 OK2016-03-23
200 OK2016-03-21
200 OK2016-03-18
200 OK2016-03-16
200 OK2016-03-14
200 OK2016-03-11
200 OK2016-03-09
200 OK2016-03-07
200 OK2016-03-04
200 OK2016-03-02
200 OK2016-02-29
200 OK2016-02-26
200 OK2016-02-24
200 OK2016-02-22
200 OK2016-02-19
200 OK2016-02-17
200 OK2016-02-15
200 OK2016-02-14
200 OK2016-02-12
200 OK2016-02-10
200 OK2016-02-08
200 OK2016-02-07
200 OK2016-02-05
200 OK2016-02-03
200 OK2016-02-01
200 OK2016-01-31
200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
200 OK2016-01-22
200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

Protein
Archaea Bacteria Eukaryota Virus
protein sequence protein structure

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Shixiang Sun [2017-03-29]
    • Shixiang Sun [2017-02-21]
    • Shixiang Sun [2017-02-13]
    • Lina Ma [2016-08-16]
    • Hongyan Yin [2016-03-31]
    • Mengwei Li [2016-02-21]
    • Mengwei Li [2016-02-15]
    • Hongyan Yin [2015-11-22]
    • Hongyan Yin [2015-06-26]
Stats