RSAPred

What is RSAPred?

RSAPred is a web server for the prediction of binding affinity of RNA-small molecule interactions, using a combination of various RNA sequence-based and small molecule structure-based features. It currently hosts machine learning models for six RNA categories namely: Aptamers, miRNAs, Repeats, Ribosomal RNAs, Riboswitches and Viral RNAs (generic and HIV TAR RNA-specific).

What is the dataset used in RSAPred?

The dataset of RNA-small molecule interactions for each RNA category in RSAPred is curated from the R-SIM database. The response variable in the dataset is the log-scale dissociation constant (pK_d) of each RNA-small molecule pair. For more information on the dataset, please visit the Statistics page of the web server.

How to identify the correct RNA category for prediction?

The RNA categories in RSAPred are predominantly based on their function. Specifically, the RNA targets considered for model development for each RNA category are provided in the RNA classification tab of the Tutorials page.

Does RSAPred consider stereochemistry of small molecules for prediction?

Yes, RSAPred considers stereochemistry of small molecules. It takes either the SMILES string (1D) or the SDF (3D) file as input through which users can provide the stereochemistry information.

Can RSAPred perform batch calculations?

No, currently RSAPred can perform binding affinity prediction for only one RNA-small molecule pair through the prediction form. However, batch calculation capabilities will be implemented in future in the server, based on user feedback.

What is the browser compatibility of RSAPred?

RSAPred is powered by HTML5, CSS, PHP, Python3 and BootstrapJS. It is best viewed in Firefox, but is also compatible with Chrome, IE10 and Opera browsers.

Can RSAPred be used for commercial purposes?

No, RSAPred is strictly released for academic and non-profit research purposes only. For more details on the terms of use, please visit the About Us page.