title: siRNAmod: A database of experimentally validated chemically modified siRNAs.
abstract: Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod.
authors.affiliation: Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39A, Chandigarh-160036, India.
authors.forename: Showkat Ahmad
authors.initials: SA
authors.lastname: Dar
authors.affiliation: Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39A, Chandigarh-160036, India.
authors.forename: Anamika
authors.initials: A
authors.lastname: Thakur
authors.affiliation: Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39A, Chandigarh-160036, India.
authors.forename: Abid
authors.initials: A
authors.lastname: Qureshi
authors.affiliation: Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research, Sector 39A, Chandigarh-160036, India.
authors.forename: Manoj
authors.initials: M
authors.lastname: Kumar
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D006801:Humans; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics; D012984:Software; D064878:Web Browser
chemical_list: D034741:RNA, Small Interfering
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