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Int. J. Mol. Sci. 2014, 15(3), 4915-4937; doi:10.3390/ijms15034915

iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking

1,2,4,* , 1
1 Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen 333046, Jiangxi, China 2 Information School, ZheJiang Textile & Fashion College, Ningbo 315211, China 3 Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia 4 Gordon Life Science Institute, 53 South Cottage Road, Belmont, MA 02478, USA
* Author to whom correspondence should be addressed.
Received: 13 January 2014 / Revised: 12 February 2014 / Accepted: 16 February 2014 / Published: 19 March 2014
(This article belongs to the Special Issue Molecular Science for Drug Development and Biomedicine)
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Nuclear receptors (NRs) are closely associated with various major diseases such as cancer, diabetes, inflammatory disease, and osteoporosis. Therefore, NRs have become a frequent target for drug development. During the process of developing drugs against these diseases by targeting NRs, we are often facing a problem: Given a NR and chemical compound, can we identify whether they are really in interaction with each other in a cell? To address this problem, a predictor called “iNR-Drug” was developed. In the predictor, the drug compound concerned was formulated by a 256-D (dimensional) vector derived from its molecular fingerprint, and the NR by a 500-D vector formed by incorporating its sequential evolution information and physicochemical features into the general form of pseudo amino acid composition, and the prediction engine was operated by the SVM (support vector machine) algorithm. Compared with the existing prediction methods in this area, iNR-Drug not only can yield a higher success rate, but is also featured by a user-friendly web-server established at, which is particularly useful for most experimental scientists to obtain their desired data in a timely manner. It is anticipated that the iNR-Drug server may become a useful high throughput tool for both basic research and drug development, and that the current approach may be easily extended to study the interactions of drug with other targets as well.
Keywords: nuclear receptors (NRs); molecular fingerprints; pseudo amino acid composition; support vector machines (SVMs) nuclear receptors (NRs); molecular fingerprints; pseudo amino acid composition; support vector machines (SVMs)
This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fan, Y.-N.; Xiao, X.; Min, J.-L.; Chou, K.-C. iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking. Int. J. Mol. Sci. 2014, 15, 4915-4937.

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