{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T18:03:26Z","timestamp":1788545006579,"version":"build-2803163510"},"reference-count":60,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T00:00:00Z","timestamp":1771372800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T00:00:00Z","timestamp":1771372800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Appl Biochem Biotechnol"],"published-print":{"date-parts":[[2026,5]]},"DOI":"10.1007\/s12010-026-05616-x","type":"journal-article","created":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T11:02:35Z","timestamp":1771412555000},"page":"3568-3590","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Strategic Computational Design of siRNA Molecules Targeting Structural Genes of SARS-CoV-2"],"prefix":"10.1007","volume":"198","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9594-3559","authenticated-orcid":false,"given":"Abhishek Kumar","family":"Mishra","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sourabh Kumar","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shilpy","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kashish","family":"Gupta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manoj Kumar","family":"Mishra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8575-6939","authenticated-orcid":false,"given":"Varun Kumar","family":"Sharma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,2,18]]},"reference":[{"issue":"13","key":"5616_CR1","doi-asserted-by":"publisher","first-page":"1199","DOI":"10.1056\/NEJMoa2001316","volume":"382","author":"Q Li","year":"2020","unstructured":"Li, Q., Guan, X., Wu, P., Wang, X., Zhou, L., Tong, Y., Ren, R., Leung, K. S. M., Lau, E. H. Y., Wong, J. Y., Xing, X., Xiang, N., Wu, Y., Li, C., Chen, Q., Li, D., Liu, T., Zhao, J., Liu, M., & Feng, Z. (2020). Early transmission dynamics in Wuhan, China, of novel coronavirus\u2013infected pneumonia. The New England Journal of Medicine, 382(13), 1199\u20131207. https:\/\/doi.org\/10.1056\/NEJMoa2001316","journal-title":"The New England Journal of Medicine"},{"key":"5616_CR2","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/j.ijsu.2020.02.034","volume":"76","author":"C Sohrabi","year":"2020","unstructured":"Sohrabi, C., Alsafi, Z., O\u2019Neill, N., Khan, M., Kerwan, A., Al-Jabir, A., Iosifidis, C., & Agha, R. (2020). World health organization declares global emergency: A review of the 2019 novel coronavirus (COVID-19). International Journal of Surgery, 76, 71\u201376. https:\/\/doi.org\/10.1016\/j.ijsu.2020.02.034","journal-title":"International Journal of Surgery"},{"issue":"7798","key":"5616_CR3","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","volume":"579","author":"P Zhou","year":"2020","unstructured":"Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B., Huang, C.-L., Chen, H.-D., Chen, J., Luo, Y., Guo, H., Jiang, R.-D., Liu, M.-Q., Chen, Y., Shen, X.-R., Wang, X., & Shi, Z.-L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270\u2013273. https:\/\/doi.org\/10.1038\/s41586-020-2012-7","journal-title":"Nature"},{"issue":"4","key":"5616_CR4","doi-asserted-by":"publisher","first-page":"418","DOI":"10.1002\/jmv.25681","volume":"92","author":"Y Chen","year":"2020","unstructured":"Chen, Y., Liu, Q., & Guo, D. (2020). Emerging coronaviruses: Genome structure, replication, and pathogenesis. Journal of Medical Virology, 92(4), 418\u2013423. https:\/\/doi.org\/10.1002\/jmv.25681","journal-title":"Journal of Medical Virology"},{"issue":"1","key":"5616_CR5","doi-asserted-by":"publisher","DOI":"10.1186\/s12985-023-01968-6","volume":"20","author":"W Wu","year":"2023","unstructured":"Wu, W., Cheng, Y., Zhou, H., Sun, C., & Zhang, S. (2023). The SARS-CoV-2 nucleocapsid protein: Its role in the viral life cycle, structure and functions, and use as a potential target in the development of vaccines and diagnostics. Virology Journal, 20(1), Article 6. https:\/\/doi.org\/10.1186\/s12985-023-01968-6","journal-title":"Virology Journal"},{"issue":"2","key":"5616_CR6","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines11020204","volume":"11","author":"R Nejat","year":"2023","unstructured":"Nejat, R., Torshizi, M. F., & Najafi, D. J. (2023). S protein, ACE2 and host cell proteases in SARS-CoV-2 cell entry and infectivity; Is soluble ACE2 a two blade sword? A narrative review. Vaccines, 11(2), Article 204. https:\/\/doi.org\/10.3390\/vaccines11020204","journal-title":"Vaccines"},{"issue":"1","key":"5616_CR7","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-52808-2","volume":"15","author":"H Yajima","year":"2024","unstructured":"Yajima, H., Anraku, Y., Kaku, Y., Kimura, K. T., Plianchaisuk, A., Okumura, K., Nakada-Nakura, Y., Atarashi, Y., Hemmi, T., Kuroda, D., Takahashi, Y., Kita, S., Sasaki, J., Sumita, H., Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito, J., Maenaka, K., Sato, K., & Hashiguchi, T. (2024). Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1. Nature Communications, 15(1), Article 8574. https:\/\/doi.org\/10.1038\/s41467-024-52808-2","journal-title":"Nature Communications"},{"key":"5616_CR8","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopha.2023.114242","volume":"159","author":"S Zhou","year":"2023","unstructured":"Zhou, S., Lv, P., Li, M., Chen, Z., Xin, H., Reilly, S., & Zhang, X. (2023). SARS-CoV-2 E protein: Pathogenesis and potential therapeutic development. Biomedicine & Pharmacotherapy, 159, Article 114242. https:\/\/doi.org\/10.1016\/j.biopha.2023.114242","journal-title":"Biomedicine & Pharmacotherapy"},{"key":"5616_CR9","unstructured":"WHO. (2025). COVID-19 Dashboard; number of COVID-19 cases reported to WHO (cumulative total). Updated on January 12 2025; Accessed on January 28 2025. https:\/\/data.who.int\/dashboards\/covid19\/cases?n=c"},{"issue":"5","key":"5616_CR10","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1007\/s40292-025-00738-5","volume":"32","author":"Z Naushad","year":"2025","unstructured":"Naushad, Z., Malik, J., Mishra, A. K., Singh, S., Shrivastav, D., Sharma, C. K., Verma, V. V., Pal, R. K., Roy, B., & Sharma, V. K. (2025). Artificial intelligence in cardiovascular health: Insights into post-COVID public health challenges. High Blood Pressure & Cardiovascular Prevention, 32(5), 475\u2013494. https:\/\/doi.org\/10.1007\/s40292-025-00738-5","journal-title":"High Blood Pressure & Cardiovascular Prevention"},{"issue":"3","key":"5616_CR11","doi-asserted-by":"publisher","DOI":"10.3390\/v15030624","volume":"15","author":"AA Al-Fattah Yahaya","year":"2023","unstructured":"Al-Fattah Yahaya, A. A., Khalid, K., Lim, H. X., & Poh, C. L. (2023). Development of next generation vaccines against SARS-CoV-2 and variants of concern. Viruses, 15(3), Article 624. https:\/\/doi.org\/10.3390\/v15030624","journal-title":"Viruses"},{"issue":"5","key":"5616_CR12","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1016\/j.jiph.2020.09.014","volume":"14","author":"VK Sharma","year":"2021","unstructured":"Sharma, V. K., Tomar, L. K., Tyagi, C., Manjhi, J., Reddy, Y. P., & Tiwari, S. K. (2021). COVID-19 and anticoagulant based therapeutics: Approach with great promise. Journal of Infection and Public Health, 14(5), 681\u2013682. https:\/\/doi.org\/10.1016\/j.jiph.2020.09.014","journal-title":"Journal of Infection and Public Health"},{"issue":"1","key":"5616_CR13","doi-asserted-by":"publisher","DOI":"10.1186\/s12929-022-00853-8","volume":"29","author":"WY Chi","year":"2022","unstructured":"Chi, W. Y., Li, Y. D., Huang, H. C., Chan, T. E. H., Chow, S. Y., Su, J. H., Ferrall, L., Hung, C. F., & Wu, T. C. (2022). COVID-19 vaccine update: Vaccine effectiveness, SARS-CoV-2 variants, boosters, adverse effects, and immune correlates of protection. Journal of Biomedical Science, 29(1), Article 82. https:\/\/doi.org\/10.1186\/s12929-022-00853-8","journal-title":"Journal of Biomedical Science"},{"key":"5616_CR14","doi-asserted-by":"publisher","unstructured":"Maillard, P. V., Veen, A. G., Poirier, E. Z., Reis, & Sousa, C. (2019). Slicing and dicing viruses: Antiviral RNA interference in mammals. The EMBO Journal, 38(8). https:\/\/doi.org\/10.15252\/embj.2018100941","DOI":"10.15252\/embj.2018100941"},{"issue":"5","key":"5616_CR15","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1007\/s40259-022-00549-3","volume":"36","author":"M Friedrich","year":"2022","unstructured":"Friedrich, M., & Aigner, A. (2022). Therapeutic siRNA: State-of-the-art and future perspectives. BioDrugs\u202f: Clinical Immunotherapeutics, Biopharmaceuticals and Gene Therapy, 36(5), 549\u2013571. https:\/\/doi.org\/10.1007\/s40259-022-00549-3","journal-title":"BioDrugs : Clinical Immunotherapeutics, Biopharmaceuticals and Gene Therapy"},{"issue":"1","key":"5616_CR16","doi-asserted-by":"publisher","DOI":"10.1007\/s12038-020-00046-1","volume":"45","author":"A Maitra","year":"2020","unstructured":"Maitra, A., Sarkar, M. C., Raheja, H., Biswas, N. K., Chakraborti, S., Singh, A. K., Ghosh, S., Sarkar, S., Patra, S., Mondal, R. K., Ghosh, T., Chatterjee, A., Banu, H., Majumdar, A., Chinnaswamy, S., Srinivasan, N., Dutta, S., & Das, S. (2020). Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. Journal of Biosciences, 45(1), Article 76. https:\/\/doi.org\/10.1007\/s12038-020-00046-1","journal-title":"Journal of Biosciences"},{"issue":"D1","key":"5616_CR17","doi-asserted-by":"publisher","first-page":"D571","DOI":"10.1093\/nar\/gku1207","volume":"43","author":"JR Brister","year":"2015","unstructured":"Brister, J. R., Ako-adjei, D., Bao, Y., & Blinkova, O. (2015). NCBI viral genomes resource. Nucleic Acids Research, 43(D1), D571\u2013D577. https:\/\/doi.org\/10.1093\/nar\/gku1207","journal-title":"Nucleic Acids Research"},{"issue":"D1","key":"5616_CR18","doi-asserted-by":"publisher","first-page":"D9","DOI":"10.1093\/nar\/gkz899","volume":"48","author":"EW Sayers","year":"2020","unstructured":"Sayers, E. W., Beck, J., Brister, J. R., Bolton, E. E., Canese, K., Comeau, D. C., Funk, K., Ketter, A., Kim, S., Kimchi, A., Kitts, P. A., Kuznetsov, A., Lathrop, S., Lu, Z., McGarvey, K., Madden, T. L., Murphy, T. D., O\u2019Leary, N., Phan, L., \u2026 Ostell, J. (2020). Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 48(D1), D9\u2013D16. https:\/\/doi.org\/10.1093\/nar\/gkz899","journal-title":"Nucleic Acids Research"},{"issue":"4","key":"5616_CR19","doi-asserted-by":"publisher","first-page":"1160","DOI":"10.1093\/bib\/bbx108","volume":"20","author":"K Katoh","year":"2019","unstructured":"Katoh, K., Rozewicki, J., & Yamada, K. D. (2019). MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics, 20(4), 1160\u20131166. https:\/\/doi.org\/10.1093\/bib\/bbx108","journal-title":"Briefings in Bioinformatics"},{"issue":"W1","key":"5616_CR20","doi-asserted-by":"publisher","first-page":"W7","DOI":"10.1093\/nar\/gkv318","volume":"43","author":"I Sela","year":"2015","unstructured":"Sela, I., Ashkenazy, H., Katoh, K., & Pupko, T. (2015). GUIDANCE2: Accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Research, 43(W1), W7\u2013W14. https:\/\/doi.org\/10.1093\/nar\/gkv318","journal-title":"Nucleic Acids Research"},{"issue":"2","key":"5616_CR21","doi-asserted-by":"publisher","first-page":"408","DOI":"10.1093\/bioinformatics\/btz576","volume":"36","author":"MC Frith","year":"2020","unstructured":"Frith, M. C. (2020). How sequence alignment scores correspond to probability models. Bioinformatics, 36(2), 408\u2013415. https:\/\/doi.org\/10.1093\/bioinformatics\/btz576","journal-title":"Bioinformatics"},{"issue":"W1","key":"5616_CR22","doi-asserted-by":"publisher","first-page":"W232","DOI":"10.1093\/nar\/gkw256","volume":"44","author":"J Trifinopoulos","year":"2016","unstructured":"Trifinopoulos, J., Nguyen, L.-T., von Haeseler, A., & Minh, B. Q. (2016). W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research, 44(W1), W232\u2013W235. https:\/\/doi.org\/10.1093\/nar\/gkw256","journal-title":"Nucleic Acids Research"},{"key":"5616_CR23","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz239","author":"I Letunic","year":"2019","unstructured":"Letunic, I., & Bork, P. (2019). Interactive tree of life (iTOL) v4: Recent updates and new developments. Nucleic Acids Research. https:\/\/doi.org\/10.1093\/nar\/gkz239","journal-title":"Nucleic Acids Research"},{"issue":"5","key":"5616_CR24","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1038\/nbt1404","volume":"26","author":"H Tafer","year":"2008","unstructured":"Tafer, H., Ameres, S. L., Obernosterer, G., Gebeshuber, C. A., Schroeder, R., Martinez, J., & Hofacker, I. L. (2008). The impact of target site accessibility on the design of effective SiRNAs. Nature Biotechnology, 26(5), 578\u2013583. https:\/\/doi.org\/10.1038\/nbt1404","journal-title":"Nature Biotechnology"},{"issue":"18","key":"5616_CR25","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm699","volume":"35","author":"M Ichihara","year":"2007","unstructured":"Ichihara, M., Murakumo, Y., Masuda, A., Matsuura, T., Asai, N., Jijiwa, M., Ishida, M., Shinmi, J., Yatsuya, H., Qiao, S., Takahashi, M., & Ohno, K. (2007). Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities. Nucleic Acids Research, 35(18), Article e123. https:\/\/doi.org\/10.1093\/nar\/gkm699","journal-title":"Nucleic Acids Research"},{"key":"5616_CR26","doi-asserted-by":"publisher","unstructured":"Kumar, A., & Chordia, N. (2015). In Silico PCR Primer Designing and Validation. In Methods in Molecular Biology (pp. 143\u2013151). https:\/\/doi.org\/10.1007\/978-1-4939-2365-6_10","DOI":"10.1007\/978-1-4939-2365-6_10"},{"issue":"10","key":"5616_CR27","doi-asserted-by":"publisher","first-page":"1805","DOI":"10.1261\/rna.1643609","volume":"15","author":"ZJ Lu","year":"2009","unstructured":"Lu, Z. J., Gloor, J. W., & Mathews, D. H. (2009). Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA, 15(10), 1805\u20131813. https:\/\/doi.org\/10.1261\/rna.1643609","journal-title":"RNA"},{"issue":"7","key":"5616_CR28","doi-asserted-by":"publisher","DOI":"10.1002\/cpz1.846","volume":"3","author":"SE Ali","year":"2023","unstructured":"Ali, S. E., Mittal, A., & Mathews, D. H. (2023). RNA secondary structure analysis using RNAstructure. Current Protocols, 3(7), Article e846. https:\/\/doi.org\/10.1002\/cpz1.846","journal-title":"Current Protocols"},{"key":"5616_CR29","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2015.053","author":"LA Kelley","year":"2015","unstructured":"Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. E. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols. https:\/\/doi.org\/10.1038\/nprot.2015.053","journal-title":"Nature Protocols"},{"issue":"1","key":"5616_CR30","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1002\/pro.3289","volume":"27","author":"RA Laskowski","year":"2018","unstructured":"Laskowski, R. A., Jab\u0142o\u0144ska, J., Pravda, L., Va\u0159ekov\u00e1, R. S., & Thornton, J. M. (2018). PDBsum: Structural summaries of PDB entries. Protein Science, 27(1), 129\u2013134. https:\/\/doi.org\/10.1002\/pro.3289","journal-title":"Protein Science"},{"issue":"1\u20133","key":"5616_CR31","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/S0014-5793(04)00087-0","volume":"560","author":"Y Zhang","year":"2004","unstructured":"Zhang, Y., Li, T., Fu, L., Yu, C., Li, Y., Xu, X., Wang, Y., Ning, H., Zhang, S., Chen, W., Babiuk, L. A., & Chang, Z. (2004). Silencing SARS-CoV Spike protein expression in cultured cells by RNA interference. FEBS Letters, 560(1\u20133), 141\u2013146. https:\/\/doi.org\/10.1016\/S0014-5793(04)00087-0","journal-title":"FEBS Letters"},{"issue":"3","key":"5616_CR32","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1021\/acscentsci.0c00272","volume":"6","author":"C Liu","year":"2020","unstructured":"Liu, C., Zhou, Q., Li, Y., Garner, L. V., Watkins, S. P., Carter, L. J., Smoot, J., Gregg, A. C., Daniels, A. D., Jervey, S., & Albaiu, D. (2020). Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases. ACS Central Science, 6(3), 315\u2013331. https:\/\/doi.org\/10.1021\/acscentsci.0c00272","journal-title":"ACS Central Science"},{"issue":"7\u20138","key":"5616_CR33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/1061186X.2020.1793990","volume":"28","author":"MM Alvi","year":"2020","unstructured":"Alvi, M. M., Sivasankaran, S., & Singh, M. (2020). Pharmacological and non-pharmacological efforts at prevention, mitigation, and treatment for COVID-19. Journal of Drug Targeting, 28(7\u20138), 1\u201313. https:\/\/doi.org\/10.1080\/1061186X.2020.1793990","journal-title":"Journal of Drug Targeting"},{"key":"5616_CR34","doi-asserted-by":"publisher","DOI":"10.1016\/j.omtn.2023.01.005","author":"Y Kuboi","year":"2023","unstructured":"Kuboi, Y., Suzuki, Y., Motoi, S., Matsui, C., Toritsuka, N., Nakatani, T., Tahara, K., Takahashi, Y., Ida, Y., Tomimatsu, A., Soejima, M., & Imai, T. (2023). Identification of potent siRNA targeting complement C5 and its robust activity in pre-clinical models of myasthenia gravis and collagen-induced arthritis. Molecular Therapy - Nucleic Acids. https:\/\/doi.org\/10.1016\/j.omtn.2023.01.005","journal-title":"Molecular Therapy - Nucleic Acids"},{"key":"5616_CR35","doi-asserted-by":"publisher","DOI":"10.1101\/2020.01.23.917559","author":"A Ebenezer","year":"2020","unstructured":"Ebenezer, A. (2020). Designing effective small interfering RNA for post-transcriptional silencing of human GREM1: A comprehensive bioinformatics approach. bioRxiv. https:\/\/doi.org\/10.1101\/2020.01.23.917559","journal-title":"bioRxiv"},{"key":"5616_CR36","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae011","author":"T Cazares","year":"2024","unstructured":"Cazares, T., Higgs, R. E., Wang, J., & Ozer, H. G. (2024). SeedMatchR: Identify off-target effects mediated by siRNA seed regions in RNA-seq experiments. Bioinformatics. https:\/\/doi.org\/10.1093\/bioinformatics\/btae011","journal-title":"Bioinformatics"},{"issue":"2","key":"5616_CR37","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1016\/S1046-2023(02)00023-3","volume":"26","author":"S Elbashir","year":"2002","unstructured":"Elbashir, S. (2002). Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods, 26(2), 199\u2013213. https:\/\/doi.org\/10.1016\/S1046-2023(02)00023-3","journal-title":"Methods"},{"issue":"4","key":"5616_CR38","doi-asserted-by":"publisher","first-page":"1050","DOI":"10.1016\/j.bbrc.2004.02.157","volume":"316","author":"M Amarzguioui","year":"2004","unstructured":"Amarzguioui, M., & Prydz, H. (2004). An algorithm for selection of functional SiRNA sequences. Biochemical and Biophysical Research Communications, 316(4), 1050\u20131058. https:\/\/doi.org\/10.1016\/j.bbrc.2004.02.157","journal-title":"Biochemical and Biophysical Research Communications"},{"issue":"3","key":"5616_CR39","doi-asserted-by":"publisher","first-page":"936","DOI":"10.1093\/nar\/gkh247","volume":"32","author":"K Ui-Tei","year":"2004","unstructured":"Ui-Tei, K. (2004). Guidelines for the selection of highly effective SiRNA sequences for mammalian and chick RNA interference. Nucleic Acids Research, 32(3), 936\u2013948. https:\/\/doi.org\/10.1093\/nar\/gkh247","journal-title":"Nucleic Acids Research"},{"issue":"3","key":"5616_CR40","doi-asserted-by":"publisher","first-page":"893","DOI":"10.1093\/nar\/gkh238","volume":"32","author":"AC Hsieh","year":"2004","unstructured":"Hsieh, A. C. (2004). A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: Determinants of gene silencing for use in cell-based screens. Nucleic Acids Research, 32(3), 893\u2013901. https:\/\/doi.org\/10.1093\/nar\/gkh238","journal-title":"Nucleic Acids Research"},{"issue":"4","key":"5616_CR41","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl1120","volume":"35","author":"T Katoh","year":"2007","unstructured":"Katoh, T., & Suzuki, T. (2007). Specific residues at every third position of siRNA shape its efficient RNAi activity. Nucleic Acids Research, 35(4), Article e27. https:\/\/doi.org\/10.1093\/nar\/gkl1120","journal-title":"Nucleic Acids Research"},{"issue":"6","key":"5616_CR42","doi-asserted-by":"publisher","first-page":"788","DOI":"10.4161\/cc.3.6.892","volume":"3","author":"S Takasaki","year":"2004","unstructured":"Takasaki, S., Kotani, S., & Konagaya, A. (2004). An effective method for selecting SiRNA target sequences in mammalian cells. Cell Cycle, 3(6), 788\u2013793. https:\/\/doi.org\/10.4161\/cc.3.6.892","journal-title":"Cell Cycle"},{"issue":"3","key":"5616_CR43","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1038\/nbt936","volume":"22","author":"A Reynolds","year":"2004","unstructured":"Reynolds, A., Leake, D., Boese, Q., Scaringe, S., Marshall, W. S., & Khvorova, A. (2004). Rational siRNA design for RNA interference. Nature Biotechnology, 22(3), 326\u2013330. https:\/\/doi.org\/10.1038\/nbt936","journal-title":"Nature Biotechnology"},{"issue":"8","key":"5616_CR44","doi-asserted-by":"publisher","first-page":"995","DOI":"10.1038\/nbt1118","volume":"23","author":"D Huesken","year":"2005","unstructured":"Huesken, D., Lange, J., Mickanin, C., Weiler, J., Asselbergs, F., Warner, J., Meloon, B., Engel, S., Rosenberg, A., Cohen, D., Labow, M., Reinhardt, M., Natt, F., & Hall, J. (2005). Design of a genome-wide SiRNA library using an artificial neural network. Nature Biotechnology, 23(8), 995\u20131001. https:\/\/doi.org\/10.1038\/nbt1118","journal-title":"Nature Biotechnology"},{"key":"5616_CR45","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-7-520","volume":"7","author":"JP Vert","year":"2006","unstructured":"Vert, J. P., Foveau, N., Lajaunie, C., & Vandenbrouck, Y. (2006). An accurate and interpretable model for siRNA efficacy prediction. BMC Bioinformatics, 7, Article 520. https:\/\/doi.org\/10.1186\/1471-2105-7-520","journal-title":"BMC Bioinformatics"},{"issue":"22","key":"5616_CR46","doi-asserted-by":"publisher","first-page":"7100","DOI":"10.1093\/nar\/gkn902","volume":"36","author":"K Ui-Tei","year":"2008","unstructured":"Ui-Tei, K., Naito, Y., Nishi, K., Juni, A., & Saigo, K. (2008). Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect. Nucleic Acids Research, 36(22), 7100\u20137109. https:\/\/doi.org\/10.1093\/nar\/gkn902","journal-title":"Nucleic Acids Research"},{"issue":"2","key":"5616_CR47","doi-asserted-by":"publisher","DOI":"10.3390\/genes13020319","volume":"13","author":"Y Kobayashi","year":"2022","unstructured":"Kobayashi, Y., Tian, S., & Ui-Tei, K. (2022). The siRNA off-target effect is determined by base-pairing stabilities of two different regions with opposite effects. Genes, 13(2), Article 319. https:\/\/doi.org\/10.3390\/genes13020319","journal-title":"Genes"},{"key":"5616_CR48","doi-asserted-by":"publisher","DOI":"10.1016\/j.imu.2021.100569","volume":"24","author":"M Hasan","year":"2021","unstructured":"Hasan, M., Ashik, A. I., Chowdhury, M. B., Tasnim, A. T., Nishat, Z. S., Hossain, T., & Ahmed, S. (2021). Computational prediction of potential siRNA and human miRNA sequences to silence orf1ab associated genes for future therapeutics against SARS-CoV-2. Informatics in Medicine Unlocked, 24, Article 100569. https:\/\/doi.org\/10.1016\/j.imu.2021.100569","journal-title":"Informatics in Medicine Unlocked"},{"issue":"1","key":"5616_CR49","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad421","volume":"25","author":"FYF Tieng","year":"2023","unstructured":"Tieng, F. Y. F., Abdullah-Zawawi, M. R., Md Shahri, N. A. A., Mohamed-Hussein, Z. A., Lee, L. H., & Mutalib, N. A. (2023). A hitchhiker\u2019s guide to RNA-RNA structure and interaction prediction tools. Briefings in Bioinformatics, 25(1), Article bbad421. https:\/\/doi.org\/10.1093\/bib\/bbad421","journal-title":"Briefings in Bioinformatics"},{"issue":"1","key":"5616_CR50","doi-asserted-by":"publisher","DOI":"10.1186\/1748-7188-1-3","volume":"1","author":"SH Bernhart","year":"2006","unstructured":"Bernhart, S. H., Tafer, H., M\u00fcckstein, U., Flamm, C., Stadler, P. F., & Hofacker, I. L. (2006). Partition function and base pairing probabilities of RNA heterodimers. Algorithms for Molecular Biology, 1(1), Article 3. https:\/\/doi.org\/10.1186\/1748-7188-1-3","journal-title":"Algorithms for Molecular Biology"},{"issue":"1 & 2","key":"5616_CR51","doi-asserted-by":"publisher","first-page":"182","DOI":"10.4103\/ijmr.IJMR_2855_20","volume":"153","author":"K Panda","year":"2021","unstructured":"Panda, K., Alagarasu, K., Cherian, S. S., & Parashar, D. (2021). Prediction of potential small interfering RNA molecules for silencing of the spike gene of SARS-CoV-2. Indian Journal of Medical Research, 153(1 & 2), 182\u2013189. https:\/\/doi.org\/10.4103\/ijmr.IJMR_2855_20","journal-title":"Indian Journal of Medical Research"},{"issue":"11","key":"5616_CR52","doi-asserted-by":"publisher","DOI":"10.1007\/s13205-023-03767-w","volume":"13","author":"PS Ramalingam","year":"2023","unstructured":"Ramalingam, P. S., & Arumugam, S. (2023). Computational design and validation of effective siRNAs to silence oncogenic KRAS. 3 Biotech, 13(11), Article 350. https:\/\/doi.org\/10.1007\/s13205-023-03767-w","journal-title":"3 Biotech"},{"key":"5616_CR53","doi-asserted-by":"publisher","unstructured":"Pandey, A. K., & Verma, S. (2021). An in Silico analysis of effective SiRNAs against COVID-19 by targeting the leader sequence of SARS\u2010CoV\u20102. Advances in cell and gene therapy, 4(2). https:\/\/doi.org\/10.1002\/acg2.107","DOI":"10.1002\/acg2.107"},{"key":"5616_CR54","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygeno.2020.12.021","author":"UF Chowdhury","year":"2021","unstructured":"Chowdhury, U. F., Sharif Shohan, M. U., Hoque, K. I., Beg, M. A., Sharif Siam, M. K., & Moni, M. A. (2021). A computational approach to design potential siRNA molecules as a prospective tool for silencing nucleocapsid phosphoprotein and surface glycoprotein gene of SARS-CoV-2. Genomics. https:\/\/doi.org\/10.1016\/j.ygeno.2020.12.021","journal-title":"Genomics"},{"issue":"6","key":"5616_CR55","doi-asserted-by":"publisher","DOI":"10.1007\/s00894-025-06402-y","volume":"31","author":"VV Verma","year":"2025","unstructured":"Verma, V. V., Vimal, S., Mishra, M. K., & Sharma, V. K. (2025). A comprehensive review on structural insights through molecular visualization: Tools, applications, and limitations. Journal of Molecular Modeling, 31(6), Article 173. https:\/\/doi.org\/10.1007\/s00894-025-06402-y","journal-title":"Journal of Molecular Modeling"},{"key":"5616_CR56","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2022.105310","volume":"102","author":"A Mahfuz","year":"2022","unstructured":"Mahfuz, A., Khan, M. A., Sajib, E. H., Deb, A., Mahmud, S., Hasan, M., Saha, O., Islam, A., & Rahaman, M. M. (2022). Designing potential siRNA molecules for silencing the gene of the nucleocapsid protein of Nipah virus: A computational investigation. Infection, Genetics and Evolution, 102, Article 105310. https:\/\/doi.org\/10.1016\/j.meegid.2022.105310","journal-title":"Infection, Genetics and Evolution"},{"key":"5616_CR57","doi-asserted-by":"publisher","DOI":"10.1080\/07391102.2020.1796811","author":"P Pandey","year":"2020","unstructured":"Pandey, P., Rane, J. S., Chatterjee, A., Kumar, A., Khan, R., Prakash, A., & Ray, S. (2020). Targeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: An in silico study for drug development. Journal of Biomolecular Structure and Dynamics. https:\/\/doi.org\/10.1080\/07391102.2020.1796811","journal-title":"Journal of Biomolecular Structure and Dynamics"},{"key":"5616_CR58","doi-asserted-by":"publisher","unstructured":"Da, A., Wu-Lu, M., Dragelj, J., Mroginski, M. A., & Ebrahimi, K. H. (2023). Multi-structural molecular Docking (MOD) combined with molecular dynamics reveal the structural requirements of designing broad-spectrum inhibitors of SARS-CoV-2 entry to host cells. Scientific Reports, 13(1). https:\/\/doi.org\/10.1038\/s41598-023-42015-2","DOI":"10.1038\/s41598-023-42015-2"},{"issue":"3","key":"5616_CR59","doi-asserted-by":"publisher","DOI":"10.1016\/j.omtn.2024.102227","volume":"35","author":"M Tuttolomondo","year":"2024","unstructured":"Tuttolomondo, M., Pham, S. T. D., Terp, M. G., Cend\u00e1n Castillo, V., Kalisi, N., Vogel, S., Langkj\u00e6r, N., Hansen, U. M., Thisgaard, H., Schr\u00f8der, H. D., Palarasah, Y., & Ditzel, H. J. (2024). A novel multitargeted self-assembling peptide-siRNA complex for simultaneous inhibition of SARS-CoV-2-host cell interaction and replication. Molecular Therapy - Nucleic Acids, 35(3), Article 102227. https:\/\/doi.org\/10.1016\/j.omtn.2024.102227","journal-title":"Molecular Therapy - Nucleic Acids"},{"issue":"11","key":"5616_CR60","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0027602","volume":"6","author":"WJ Pan","year":"2011","unstructured":"Pan, W. J., Chen, C. W., & Chu, Y. W. (2011). SiPRED: Predicting siRNA efficacy using various characteristic methods. PLoS ONE, 6(11), Article e27602. https:\/\/doi.org\/10.1371\/journal.pone.0027602","journal-title":"PLoS ONE"}],"container-title":["Applied Biochemistry and Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s12010-026-05616-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s12010-026-05616-x","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s12010-026-05616-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T08:17:18Z","timestamp":1777882638000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s12010-026-05616-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,18]]},"references-count":60,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,5]]}},"alternative-id":["5616"],"URL":"https:\/\/doi.org\/10.1007\/s12010-026-05616-x","relation":{},"ISSN":["0273-2289","1559-0291"],"issn-type":[{"value":"0273-2289","type":"print"},{"value":"1559-0291","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,18]]},"assertion":[{"value":"4 February 2026","order":1,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 February 2026","order":2,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no conflicts of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of Interest"}},{"value":"The current study was conducted using computational approaches and does not involve any experiments on humans, animals, or cell types at any level. Therefore, ethical approval is not required.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical Statement"}}]}}