NDLI: Development and implementation of a novel computational tool for an efficient construction of drug-target interactome

Content Provider	IEEE Xplore Digital Library
Author	Jingchun Sun Hart, P. Zhongming Zhao
Copyright Year	2011
Description	Author affiliation: Department of Biomedical Engineering, Vanderbilt University School of Medicine, Nashville, TN 37232, USA (Hart, P.) \|\| Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA (Jingchun Sun; Zhongming Zhao)
Abstract	The application of network concepts to pharmacology has become popular and promising for better understanding the molecular mechanisms of drug actions. In this study, we developed a computational pipeline in order to construct the drug-target interactome, thereby facilitating these drug action investigations. The interactome includes drug-drug, drug-target and target-protein interaction networks. The pipeline first extracts human protein-protein interaction (PPI) data from the Protein Interaction Network Analysis (PINA) platform to obtain the cleaned human PPIs with experimental evidence. Next, the pipeline retrieves the drugs of interest, their targets and the adverse drug interactions from the DrugBank database. Based on the cleaned human PPIs and drug-related information, the pipeline finally generates three subnetworks involved in the drug-target interactome: drug-drug network, drug-target network, and target-protein interaction network. We implemented the pipeline within two Python packages. To illustrate how the pipeline works, we used schizophrenia as a keyword to obtain SZ-related drugs. The Python packages and example data are available at http://bioinfo.mc.vanderbilt.edu/software.html.
Starting Page	274
Ending Page	279
File Size	908683
Page Count	6
File Format	PDF
ISBN	9781457716126
e-ISBN	9781457716133
DOI	10.1109/BIBMW.2011.6112387
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-11-12
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Drugs Proteins Databases Pipelines Humans Data mining
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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