- Young-Cheul Shin, Soo-Yong Shin, Insuk So, Dongseop Kwon, and Ju-Hong Jeon. "TRIP Database: a manually curated database of protein–protein interactions for mammalian TRP channels." Nucleic acids research 39, no. suppl 1 (2011): D356-D361.
- Young-Cheul Shin, Soo-Yong Shin, Jung Nyeo Chun, Hyeon Sung Cho, Jin Muk Lim, Hong-Gee Kim, Insuk So, Dongseop Kwon, and Ju-Hong Jeon. "TRIP Database 2.0: A Manually Curated Information Hub for Accessing TRP Channel Interaction Network." PloS one 7, no. 10 (2012): e47165.
TRIP Database 2.0
a manually curated database of protein-protein interactions for mammalian TRP channels
Transient receptor potential (TRP) channels are a family of Ca2+-permeable cation channels. In response to a wide range of cellular stimuli, they produce electrochemical signals via membrane potential or intracellular [Ca2+]. more info
The current version of the TRIP Database documentsmore info
Major updates in the TRIP Database 2.0:
- The database contents have updated by manually curating the new publications: 33% increase in the number of indexed articles (369 from 277 peer-reviewed publications), 32% increase in the number of PPI pairs (646 from 490 PPI pairs), and 33% increase in the number of cellular proteins (394 from 297 proteins). In addition, the supplementary data of all referred articles are also scrutinized and curated.
- The database contents can be downloaded as a MS Excel format or a sif format for network visualization and analysis using "Cytoscape (http://www.cytoscape.org)".
- Users can make comments on each web page, which enables interactive communication.
- Users can print each page content of the database.
- The search system presents information from "Pubmed (http://www.ncbi.nlm.nih.gov/pubmed)" and "PIE the search (http://www.ncbi.nlm.nih.gov/IRET/PIE)" which is the specialized search engine for PPI-related articles as well as information shown in previous version.
- Users easily grasp overall PPI information through PPI matrix table according to TRP channel subfamily.
- Accessibility to relevant information has been improved various ways: mouse-over pop-up help messages and integration of new information sources, including GO (Gene Ontology) terms and disease information from OMIM (Online Mendelian Inheritance in Man).
- Transporter Classification Database (http://www.tcdb.org)
- Human Membrane Transporter Database (http://lab.digibench.net/transporter)
- IUBMB Membrane Transport Protein Nomenclature (http://www.chem.qmul.ac.uk/iubmb/mtp)
- TransportDB (http://www.membranetransport.org)
- ΔG prediction of transmembrane helix insertion (http://dgpred.cbr.su.se)
- Transmembrane helix prediction (http://www.csbio.sjtu.edu.cn/bioinf/MemBrain)
- Prediction of membrane protein topology and signal peptides (http://octopus.cbr.su.se)
- Domains and Motifs in Transmembrane Proteins (http://topdom.enzim.hu/?m=search&by=seq)
- Classification and Secondary Structure Prediction of Membrane Proteins (http://bp.nuap.nagoya-u.ac.jp/sosui)
- Wikipedia: Transient receptor potential channel-interacting protein database
We cordially thank many members of the Korean Physiology Society and the Korean Society for Ion Channel Research for helpful discussions and comments on database contents and user-interfaces.