Swiss-Prot: Juggling between evolution and stability

By Amos Bairoch, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger. 2004

384 citations recorded by the source corpus.

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In Molecular Biology

Citations in the corpus

ProGen: Language Modeling for Protein Generation (2020, methodology): “We curate the protein sequences and associated tags available in Uniparc [24], UniprotKB [7], SWISS-PROT [6], TrEMBL [10], Pfam [8], and NCBI taxonomic information [16].”
Infrastructure for the life sciences: design and implementation of the UniProt website (2009, neutral): “…online resources) (cid:129) Cross-references (cid:129) Entry information (Meta data including release dates and version numbers) (cid:129) Relevant documents (List of documents that reference an entry) Describing the information found in UniProtKB/Swiss-Prot [4] is outside the scope of this paper.”
A survey of best practices for RNA-seq data analysis (2016, background): “Protein-coding transcripts can be functionally annotated using orthology by searching for similar sequences in protein databases such as SwissProt [114] and in databases that contain conserved protein domains such as Pfam [115] and InterPro [116].”
UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View. (2016, methodology): “In addition to the preliminary information given by the submitters, UniProtKB/TrEMBL entries are processed according to automatic annotation procedures such as (1) transfer of domains and functional sites from well-characterized UniProtKB/Swiss-Prot entries belonging to protein family groups defined”
Constructing Datasets for Multi-hop Reading Comprehension Across Documents (2017, neutral): “P ROT (Bairoch et al., 2004).”
PredictProtein—an open resource for online prediction of protein structural and functional features (2014, positive): “Database searches: sequences similar to the query are identified by standard, pairwise BLAST (8) and iterated PSI-BLAST (7) searches (9,10) against a non-redundant combination of PDB (11), Swiss-Prot (12) and TrEMBL (1).”
Editing modifies the GABAA receptor subunit α3 (2007, methodology): “For the protein sequence of Gabra-3, Swiss-Prot (Bairoch et al. 2004), entry P26049, was used.”
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins (2006, background): “PROSITE signatures form a high quality collection and are closely tied to the UniProtKB/Swiss-Prot (3,4) annotation process.”
Rules for nuclear localization sequence recognition by karyopherin beta 2. (2006, positive): “R/K/H-X1–5-P-Y and human proteins in the UniProtKB/ Swiss-Prot protein database (Bairoch et al., 2004).”