LocDB

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LocDB
Database.png
Content
Description experimental annotations of localization
Organisms Homo sapiens
Arabidopsis thaliana
Contact
Research center Columbia University
Laboratory Department of Biochemistry and Molecular Biophysics
Authors Shruti Rastogi
Primary citation Rastogi & al. (2011)[1]
Release date 2010
Access
Data format MySQL database
Website http://www.rostlab.org/services/locDB
Web service URL http://www.rostlab.org/services/locDB/search.php
Miscellaneous
Version Release 1.0

LocDB[1] is an expert-curated database that collects experimental annotations for the subcellular localization of proteins in Homo sapiens (human) and Arabidopsis thaliana (Weed). The database also contains predictions of subcellular localization from a variety of state-of-the-art prediction methods for all proteins with experimental information.

Proteins are the fundamental functional components of cells. They are responsible for transforming genetic information into physical reality. These macromolecules mediate gene regulation, enzymatic catalysis, cellular metabolism, DNA replication, and transport of nutrients, recognition, and transmission of signals. The interpretation of this wealth of data to elucidate protein function in post-genomic era is the a fundamental challenge. To date, even for the most well-studied organisms such as yeast, about one-fourth of the proteins remain uncharacterized. A major obstacle in experimentally determining protein function is that the studies require enormous resources. Hence, the gap between the amount of sequences deposited in databases and the experimental characterization of the corresponding proteins is ever-growing. Bioinformatics plays a central role in bridging this sequence-function gap through the development of tools for faster and more effective prediction of protein function. This repository effectively fills the gap between experimental annotations and predictions and provides a bigger and more reliable dataset for the testing of new prediction methods.[1]

See also[edit]

References[edit]

  1. ^ a b c Rastogi, Shruti; Rost Burkhard (Jan 2011). "LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana". Nucleic Acids Res. England. 39 (Database issue): D230–4. doi:10.1093/nar/gkq927. PMC 3013784Freely accessible. PMID 21071420.