The Transporter Classification Database (TCDB): recent advances

By Milton H. Saier Jr., Vamsee S. Reddy, Brian V. Tsu, Muhammad Saad Ahmed, Ph.D., Chun Li, Gabriel Moreno-Hagelsieb. Nucleic Acids Res., 2015

665 citations recorded by the source corpus.

The Transporter Classification Database (TCDB; http://www.tcdb.org) is a freely accessible reference database for transport protein research, which provides structural, functional, mechanistic, evolutionary and disease/medical information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB). It consists of more than 10 000 non-redundant transport systems with more than 11 000 reference citations, classified into over 1000 transporter families. Transporters in TCDB can be single or multi-component systems, categorized in a functional/phylogenetic hierarchical system of classes, subclasses, families, subfamilies and transport systems. TCDB also includes updated software designed to analyze the distinctive features of transport proteins, extending its usefulness. Here we present a comprehensive update of the database contents and features and summarize recent discoveries recorded in TCDB.

Subfields: Molecular Biology, Oncology

View Paper: https://www.semanticscholar.org/paper/537ab55f4bdfcbe83ab68b2032d83ae9c7d55d31

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Peter D. Karp
2. Markus Krummenacker
3. Ron Caspi
4. Suzanne M. Paley
5. Vamsee S. Reddy
6. Gabriel Moreno-Hagelsieb
7. Carol A. Fulcher
8. Anna Gaulton

In Oncology

1. Vamsee S. Reddy
2. Dorjee G. Tamang
3. Gabriel Moreno-Hagelsieb

Citations in the corpus

• The Transporter Classification Database (2013, methodology): “(5) Made the TMSTATS Program (13) available for analyzing topological (TMS) statistics using three different topological prediction programs, HMMTOP (14), MEMSAT (15) and SPOCTUPUS (16), giving histograms of TMS distribution for any protein or for any TC class, subclass, family, subfamily or any com”
• The Transporter Classification Database (TCDB): 2021 update (2020, background): “This represents an overall growth of over 50% relative to our 2016 report (9).”
• The ChEMBL database in 2017 (2016, methodology): “Improvements have been made to the existing protein family classification for ion channels and transporters to more closely align the ChEMBL system with other resources (the IUPHAR/BPS Guide To PHARMACOLOGY (28) and TCDB (29)) and new classes have been introduced for epigenetic regulators (following”
• The EcoCyc database: reflecting new knowledge about Escherichia coli K-12 (2016, background): “The class ‘a transporter’ within EcoCyc now contains 6 child classes (Figure 1) plus numerous sub-classes, named according to IUBMB recommendations as based on the Transporter Classification Database (9).”