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GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction.

Biomedical Sciences Research Institute Computer Science Research Institute Environmental Sciences Research Institute Nanotechnology & Advanced Materials Research Institute

Browne, Fiona, Wang, Haiying, Zheng, Huiru and Azuaje, Francisco (2009) GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction. Source code for biology and medicine, 4 . p. 2. [Journal article]

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Abstract

ABSTRACT: BACKGROUND: Information 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. RESULTS: GRIP (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. CONCLUSION: GRIP 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 http://rosalind.infj.ulst.ac.uk/GRIP/.

Item Type:Journal article
Faculties and Schools:Faculty of Computing & Engineering
Faculty of Computing & Engineering > School of Computing and Mathematics
Research Institutes and Groups:Computer Science Research Institute > Artificial Intelligence and Applications
Computer Science Research Institute > Smart Environments
ID Code:9079
Deposited By:Dr Huiru Zheng
Deposited On:03 Feb 2010 10:29
Last Modified:03 Feb 2010 10:29

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