The Transporter Classification Database: recent advances
By Milton H. Saier Jr., M. Yen, Keith Noto, Dorjee G. Tamang, Charles Peter Elkan. Nucleic Acids Res., 2008
383 citations recorded by the source corpus.
The Transporter Classification Database (TCDB), freely accessible at http://www.tcdb.org, is a relational database containing sequence, structural, functional and evolutionary information about transport systems from a variety of living organisms, based on the International Union of Biochemistry and Molecular Biology-approved transporter classification (TC) system. It is a curated repository for factual information compiled largely from published references. It uses a functional/phylogenetic system of classification, and currently encompasses about 5000 representative transporters and putative transporters in more than 500 families. We here describe novel software designed to support and extend the usefulness of TCDB. Our recent efforts render it more user friendly, incorporate machine learning to input novel data in a semiautomatic fashion, and allow analyses that are more accurate and less time consuming. The availability of these tools has resulted in recognition of distant phylogenetic relationships and tremendous expansion of the information available to TCDB users.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/cbd499a34475b9fb493303b4ea3ab391e3aba7f2
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Citations in the corpus
- PDBTM: Protein Data Bank of transmembrane proteins after 8 years (2012, background): “(iii) The Transporter Classification Database (15) is a web accessible, curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from a variety of living organisms.”
- The Transporter Classification Database (TCDB): recent advances (2015, methodology): “Earlier versions of the TC database (TCDB) have been described in previous publications in Nucleic Acids Research (7,9,10).”
- A glimpse of structural biology through X-ray crystallography. (2014, background): “These unanticipated structural findings led to reclassification of membrane transporters, with nine LeuT-fold families now grouped together to constitute the APC superfamily (Saier et al., 2009).”
- BacMet: antibacterial biocide and metal resistance genes database (2013, methodology): “Subsequently, metadata, such as source organism, location (plasmid/chromosomal) and gene description, were collected from NCBI GenBank and nonredundant protein database, UniprotKB and the Transporter Classification Database (34) and included into the database covering genes with experimentally confi”
- IMG: the integrated microbial genomes database and comparative analysis system (2011, background): “A fused gene (fusion) is defined as a gene that is formed from the composition (fusion) of two or more previously separate genes (20).”