Abstract
BackgroundInformation about protein interaction networks is fundamental to understanding protein function and cellular processes. Interaction patterns among proteins can suggest new drug targets and aid in the design of new therapeutic interventions. Efforts have been made to map interactions on a proteomic-wide scale using both experimental and computational techniques. Reference datasets that contain known interacting proteins (positive cases) and non-interacting proteins (negative cases) are essential to support computational prediction and validation of protein-protein interactions. Information on known interacting and non interacting proteins are usually stored within databases. Extraction of these data can be both complex and time consuming. Although, the automatic construction of reference datasets for classification is a useful resource for researchers no public resource currently exists to perform this task.ResultsGRIP (Gold Reference dataset constructor from Information on Protein complexes) is a web-based system that provides researchers with the functionality to create reference datasets for protein-protein interaction prediction in Saccharomyces cerevisiae. Both positive and negative cases for a reference dataset can be extracted, organised and downloaded by the user. GRIP also provides an upload facility whereby users can submit proteins to determine protein complex membership. A search facility is provided where a user can search for protein complex information in Saccharomyces cerevisiae.ConclusionGRIP is developed to retrieve information on protein complex, cellular localisation, and physical and genetic interactions in Saccharomyces cerevisiae. Manual construction of reference datasets can be a time consuming process requiring programming knowledge. GRIP simplifies and speeds up this process by allowing users to automatically construct reference datasets. GRIP is free to access at .
Highlights
Information about protein interaction networks is fundamental to understanding protein function and cellular processes
Using a Gold Standard obtained from Munich Database of Interacting Proteins (MIPS) [6] and Saccharomyces Genome Database (SGD) their study demonstrated that the consolidated dataset is of greater accuracy than the individual sets and is comparable to protein-protein interactions (PPI) defined using more reliable, small-scale experimental methodologies
The MIPS complex catalogue was selected as a source for Gold Standard construction as it contains lists of known protein complexes based on data collected from validated, small-scale studies obtained from the biomedical literature
Summary
GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction. Address: 1School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK and 2Laboratory of Cardiovascular Research, Research Centre for Public Health (CRP-Santé), 1A rue Thomas Edison, Strassen L-1445, Luxembourg. Published: 26 January 2009 Source Code for Biology and Medicine 2009, 4:2 doi:10.1186/1751-0473-4-2
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