Software under Development
Pipeline for in silico Selection of RNA Aptamers

In recent years, RNA aptamers emerged as a new approach for the molecular recognition in numerous chemical and biological sensing systems. The aim of this project is to develop a computational pipeline that uses a database of short RNA structural templates for in vitro selection of RNA aptamers. The assembled pipeline will generate a tertiary RNA structure from a given sequence and will then apply the DOVIS pipeline [1,2] to screen RNA structures to the desired small molecule. The highest-scored RNA molecules will be selected for experimental in vitro screening and validation.

[1]Zhang, S., K. Kumar, X. Jiang, A. Wallqvist, and J. Reifman. DOVIS: An implementation for high-throughput virtual screening using AutoDock. BMC Bioinformatics. 2008 February 29; 9:126.
[2]Jiang, X., K. Kumar, X. Hu, A. Wallqvist, and J. Reifman. DOVIS 2.0: An efficient and easy to use parallel virtual screening tool based on AutoDock 4.0. Chem Cent J. 2008 Sep 8; 2(1):18.