biostudies-literature00400Unknown44(4)Kharma NWe present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemented procedure, which takes into consideration multiple objectives leading to a multi-objective ranking of the computer-generated ribozymes. Many ribozymes were assayed and validated, including four ribozymes targeting the transcript of a disease-causing gene (a mutant version of PABPN1). These four ribozymes were successfully tested in vitro and in vivo, for their ability to cleave the targeted transcript. The wet-lab positive results of the test are presented here demonstrating the real-world potential of both hammerhead ribozymes and RiboSoft. RiboSoft is freely available at the website http://ribosoft.fungalgenomics.ca/ribosoft/.Nucleic acids researche39https://www.ebi.ac.uk/biostudies/studies/S-EPMC4770207biostudies-literatureAutomated design of hammerhead ribozymes and validation by targeting the PABPN1 gene transcript.PMC4770207Ambri AOuellet JEhdaeivand MRRouleau GBelmonte GPerreault JNajeh SVarin LAbu-Baker AKharma N40falseAutomated design of hammerhead ribozymes and validation by targeting the PABPN1 gene transcript.We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemented procedure, which takes into consideration multiple objectives leading to a multi-objective ranking of the computer-generated ribozymes. Many ribozymes were assayed and validated, including four ribozymes targeting the transcript of a disease-causing gene (a mutant version of PABPN1). These four ribozymes were successfully tested in vitro and in vivo, for their ability to cleave the targeted transcript. The wet-lab positive results of the test are presented here demonstrating the real-world potential of both hammerhead ribozymes and RiboSoft. RiboSoft is freely available at the website http://ribosoft.fungalgenomics.ca/ribosoft/.2016-01-01T00:00:00Z2016 Feb2024-11-09T12:15:56.221Z2019-03-27T02:10:04ZS-EPMC47702072652773010.1093/nar/gkv1111