catRAPID
http://s.tartaglialab.com/page/catrapid_group

catRAPID，一个专门用来计算蛋白和RNA结合特性的工具，该工具通过整合secondary structure, hydrogen bonding , van der Waals contributions来预测蛋白和RNA的结合可能性。该网站主要有“catRAPID fragments”、“catRAPID strength”、“catRAPID omics”、“catRAPID express”、“catRAPID signature”、“catRAPID interactions with large RNAs”，一共6个不同的分析模块。

其中，catRAPID omics用于预测某一RNA（或蛋白）的结合蛋白（或RNA），可预测出大量候选，这一模块对科研工作者很实用，其他模块用于进一步分析和评估某一特定RNA与某一特定蛋白的相互结合关系，包括结合位点、相互作用倾向等等。

经典文章案例：
1. Guilin Li et al. Long noncoding RNA MRAK009713 is a novel regulator of neuropathic pain in rats. PAIN. 2017.
2. Lesca M. Holdt et al. Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans. Nature communications. 2016.
3. Shuangmei Liu et al. LncRNA NONRATT021972 siRNA regulates neuropathic pain behaviors in type 2 diabetic rats through the P2X7 receptor in dorsal root ganglia. .Molecular Brain .2016.
3. Jasmine JC Blondeau et al.  Identification of novel long non-coding RNAs in clear cell renal cell carcinoma. Clinical Epigenetics . 2015.
4. Davide Cirillo et al. Discovery of protein–RNA networks. Molecular BioSystems. 2014.
5. Davide Cirillo et al. Constitutive patterns of gene expression regulated by RNA-binding proteins. Genome Biology. 2014.
6. Davide Cirillo et al. Neurodegenerative diseases: Quantitative predictions of protein− RNA interactions. RNA. 2013.
7. Federico Agostini et al. X-inactivation: quantitative predictions of protein interactions in the Xist network. Nucleic Acids Research. 2013.
8. Davide Cirillo et al. Predictions of protein–RNA interactions. WIREs Comput Mol Sci. 2012.
9. Sylvain Maenner et al. 2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association. PLoS Biology. 2010