lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics.
Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. We provided lncRNATargets, which is a web-based platform for lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together. lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/ .
1 Beijing Key Laboratory of Innovative, Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, P. R. China.|2 Key Laboratory of Bioactive Substances and Resource, Utilization of Chinese Herbal Medicine, Ministry of Education, P. R. China.|3 Zhongguancun Open Laboratory of the Research and Development of Natural Medicine and Health Products, P. R. China.
Ruifeng
0000-0001-5549-3082
R
Hu
1 Beijing Key Laboratory of Innovative, Drug Discovery of Traditional Chinese Medicine (Natural Medicine) and Translational Medicine, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, P. R. China.|2 Key Laboratory of Bioactive Substances and Resource, Utilization of Chinese Herbal Medicine, Ministry of Education, P. R. China.|3 Zhongguancun Open Laboratory of the Research and Development of Natural Medicine and Health Products, P. R. China.
Xiaobo
X
Sun
D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D062085:RNA, Long Noncoding / Q000737:chemistry* / Q000378:metabolism*; D015203:Reproducibility of Results; D012984:Software; D013816:Thermodynamics; D014584:User-Computer Interface
D062085:RNA, Long Noncoding
Long noncoding RNAs; nucleic acid thermodynamics; target prediction; web-based platform