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Literature DB >> 33481821

PFRED: A computational platform for siRNA and antisense oligonucleotides design.

Simone Sciabola¹, Hualin Xi², Dario Cruz^1,3, Qing Cao⁴, Christine Lawrence⁵, Tianhong Zhang⁵, Sergio Rotstein⁵, Jason D Hughes⁶, Daniel R Caffrey⁷, Robert V Stanton⁸.

Abstract

PFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading at https://github.com/pfred/pfred-gui/releases/tag/v1.0 as a java Jar file. The source code and the links for downloading the precompiled version can be found at https://github.com/pfred.

Entities: Chemical Disease Gene Species

Year: 2021 PMID： 33481821 PMCID： PMC7822268 DOI： 10.1371/journal.pone.0238753

Source DB: PubMed Journal: PLoS One ISSN： 1932-6203 Impact factor: 3.240

51 in total

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Journal: Genes Dev Date: 2001-01-15 Impact factor: 11.361

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Authors: Fatima Akdim; Maartje E Visser; Diane L Tribble; Brenda F Baker; Erik S G Stroes; Rosie Yu; Joann D Flaim; John Su; Evan A Stein; John J P Kastelein
Journal: Am J Cardiol Date: 2010-03-30 Impact factor: 2.778

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Authors: Alistair M Chalk; Erik L L Sonnhammer
Journal: Bioinformatics Date: 2002-12 Impact factor: 6.937

5. Efficient prediction of siRNAs with siRNArules 1.0: an open-source JAVA approach to siRNA algorithms.

Authors: Torgeir Holen
Journal: RNA Date: 2006-07-26 Impact factor: 4.942

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Authors: Jeff Milton; Tianhong Zhang; Claire Bellamy; Eric Swayze; Christopher Hart; Markus Weisser; Sabrina Hecht; Sergio Rotstein
Journal: J Chem Inf Model Date: 2017-05-19 Impact factor: 4.956

7. HELM: a hierarchical notation language for complex biomolecule structure representation.

Authors: Tianhong Zhang; Hongli Li; Hualin Xi; Robert V Stanton; Sergio H Rotstein
Journal: J Chem Inf Model Date: 2012-09-26 Impact factor: 4.956

8. Pharmacokinetics and Pharmacodynamics of the Small Interfering Ribonucleic Acid, Givosiran, in Patients With Acute Hepatic Porphyria.

Authors: Sagar Agarwal; Amy R Simon; Varun Goel; Bahru A Habtemariam; Valerie A Clausen; Jae B Kim; Gabriel J Robbie
Journal: Clin Pharmacol Ther Date: 2020-03-07 Impact factor: 6.875

PFRED: A computational platform for siRNA and antisense oligonucleotides design.

1. RNA interference is mediated by 21- and 22-nucleotide RNAs.

2. ODNBase--a web database for antisense oligonucleotide effectiveness studies. Oligodeoxynucleotides.

3. Effect of mipomersen, an apolipoprotein B synthesis inhibitor, on low-density lipoprotein cholesterol in patients with familial hypercholesterolemia.

4. Computational antisense oligo prediction with a neural network model.

5. Efficient prediction of siRNAs with siRNArules 1.0: an open-source JAVA approach to siRNA algorithms.

6. HELM Software for Biopolymers.

7. HELM: a hierarchical notation language for complex biomolecule structure representation.

8. Pharmacokinetics and Pharmacodynamics of the Small Interfering Ribonucleic Acid, Givosiran, in Patients With Acute Hepatic Porphyria.

9. Thermodynamic calculations and statistical correlations for oligo-probes design.

10. siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect.

Review 1. Delivering the Promise of Gene Therapy with Nanomedicines in Treating Central Nervous System Diseases.

2. Evitar: designing anti-viral RNA therapies against future RNA viruses.

Review 3. The Challenges and Strategies of Antisense Oligonucleotide Drug Delivery.