Software

Inforna

A small molecule lead identification strategy for RNA targets

The Inforna server is freely available for academic use.  Please fill out the software license agreement and return a signed copy to disney@scripps.edu.  A user name and password will then be provided.

A description of Inforna can be found in: Velagapudi SP, Gallo SM, and Disney MD. Sequence-based design of bioactive small molecules that target precursor microRNAs. Nature Chemical Biology, 2014, 10, 291-297, doi: 10.1038/nchembio.1452

microRNA Motif Database

a database of motifs found in human microRNAs

The microRNA database is freely available for academic use.  Please fill out the software license agreement and return a signed copy to disney@scripps.edu.  A user name and password will then be provided.

A description of microRNA motif database can be found in: Liu B, Childs-Disney JL, Znosko BM, Wang D, Fallahi M, Gallo SM, and Disney MD.  Analysis of human pre-microRNA secondary structural elements.  2015, in press.

RNA-PSP

Software to identify privileged RNA space using sequence information

Available for download by using the link below.

Descriptions of RNA-PSP can be found in: Paul DJ, Seedhouse SJ, and Disney MD.  Two-dimensional combinatorial screening and the RNA Privileged Space Predictor (RNA-PSP) efficiently identify aminoglycoside-RNA hairpin loop interactions. Nucleic Acids Research, (2009), 37, 5894-5907; and

Velagapudi SP, Seedhouse SJ, Disney MD. Structure-activity relationships through sequencing (StARTS) defines optimal and suboptimal RNA motif targets for small molecules.  Angewandte Chemie International Edition, English (2010), 49, 3816-3818.

Link to download both versions of RNA-PSP

Chem-PSP

Software to identify privilege chemical space that binds RNA motifs

Available for download by using the link below.

A description of Chem-PSP can be found in: Seedhouse SJ, Labuda LP, Disney MD.  The Privileged Chemical Space Predictor (PCSP): a computer program that identifies privileged chemical space from screens of modularly assembled chemical libraries. Bioorganic Medicinal Chemistry Letters (2010), 20, 1338-1343.

Link to download Chem-PSP