SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

By S. Velankar, J. M. Dana, Julius O. B. Jacobsen, G. V. Ginkel, P. Gane, Jie Luo, Thomas J. Oldfield, C. O’Donovan, Maria Jesus Martin, Gerard J. Kleywegt. 2012

296 citations recorded by the source corpus.

The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This process is carried out for every weekly PDB release and the information is stored in the SIFTS database. The SIFTS process includes cross-references to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database. The information is exported in XML format, one file for each PDB entry, and is made available by FTP. Many bioinformatics resources use SIFTS data to obtain cross-references between the PDB and other biological databases so as to provide their users with up-to-date information.

Subfields: Computational Biology & Bioinformatics

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Citations in the corpus

GPCRdb in 2021: integrating GPCR sequence, structure and function (2020, methodology): “The Structure Constructs section in GPCRdb integrates GPCR structure sequence from PDB, residue annotations from SIFTS (35) and an extensive manual literature annotation of mutation effects and inserts (e.g. purification tags) as well as experimental methods and reagents for GPCR structure determina”
The SWISS-MODEL Repository—new features and functionality (2016, methodology): “Homology models are generated using the automated SWISS-MODEL (13) homology modeling server pipeline, and experimental structures of proteins are mapped between the PDB and UniProtKB using SIFTS (14).”
Modeling aspects of the language of life through transfer-learning protein sequences (2019, methodology): “Functions encoded by the Enzyme Commission number (E.C., [60]) were retrieved via the “ Structure Integration with Function, Taxonomy and Sequence ” (SIFTS) mapping [61].”
The Pfam protein families database: towards a more sustainable future (2015, methodology): “Another advantage is that we can use our pre-existing method to map Pfam entries to known structures using the SIFTS mapping (9) between UniProtKB and PDB accessions.”
InterPro in 2019: improving coverage, classification and access to protein sequence annotations (2018, methodology): “Structures are imported from the SIFTS (32) mapping provided by PDBe.”
Gene3D: Extensive prediction of globular domains in proteins (2017, methodology): “The protein sequence viewer now also optionally displays CATH-PDB domain architectures (i.e. direct CATH chop-pings of the PDB mapped onto the protein sequence by SIFTS (11)), allowing us to check how the Gene3D domain assignments compare to the known annotations contained in CATH.”
PDBsum additions (2013, methodology): “We used the mappings in UniProtKB (8) between the Ensembl transcript (9) and the UniProt identifier before identifying the corresponding position in the protein structure via SIFTS (10).”
Modeling the language of life – Deep Learning Protein Sequences (2019, methodology): “, [55]) were retrieved via 6 the "Structure Integration with Function, Taxonomy and Sequence” (SIFTS) mapping [56].”
The RCSB protein data bank: integrative view of protein, gene and 3D structural information (2016, methodology): “To provide the most up-to-date link from pathway to PDB, we update the underlying data on a weekly basis using the UniProt to PDB mappings are available from the SIFTS initiative (26).”
Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis (2013, methodology): “First, PFAM domains present in each protein A were identified using the mappings provided by the PDB and SIFTS (25) databases (e.g.”
An Online Resource for GPCR Structure Determination and Analysis (2019, background): “This unique ‘structure construct databank’ integrates all the GPCR structures in the PDB 22 and residue annotations from SIFTS 23 , plus an extensive manual literature annotation of mutation effects and terminal inserts that t a T nee r a c e a m i ne i no i F r e e f a tt y a c i d i n i n l e cys…”