{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T13:39:42Z","timestamp":1775741982129,"version":"3.50.1"},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,7,23]],"date-time":"2025-07-23T00:00:00Z","timestamp":1753228800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,7,23]],"date-time":"2025-07-23T00:00:00Z","timestamp":1753228800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100004515","name":"Universiti Kebangsaan Malaysia","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004515","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1007\/s10822-025-00633-0","type":"journal-article","created":{"date-parts":[[2025,7,23]],"date-time":"2025-07-23T03:53:11Z","timestamp":1753242791000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Molecular dynamics simulations reveal mechanistic insights into aptamer-induced structural rearrangements in viral capsid proteins"],"prefix":"10.1007","volume":"39","author":[{"given":"Chen Fei","family":"Low","sequence":"first","affiliation":[]},{"given":"Norazli","family":"Ghadin","sequence":"additional","affiliation":[]},{"given":"Muhamad Arif","family":"Mohamad Jamali","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,7,23]]},"reference":[{"key":"633_CR1","doi-asserted-by":"publisher","first-page":"738670","DOI":"10.1016\/j.aquaculture.2022.738670","volume":"561","author":"H Ganesan","year":"2022","unstructured":"Ganesan H, Ho KL, Mariatulqabtiah AR, Yong CY, Wong CL, Goh ZH et al (2022) Virus-like particles of Macrobrachium rosenbergii nodavirus: particle size and capsid protein assembly domain. Aquaculture 561:738670","journal-title":"Aquaculture"},{"issue":"4","key":"633_CR2","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1021\/acsinfecdis.1c00546","volume":"8","author":"B Chakraborty","year":"2022","unstructured":"Chakraborty B, Das S, Gupta A, Xiong Y, TV V, Kizer ME et al (2022) Aptamers for viral detection and Inhibition. ACS Infect Dis 8(4):667\u2013692","journal-title":"ACS Infect Dis"},{"key":"633_CR3","doi-asserted-by":"publisher","first-page":"785318","DOI":"10.3389\/fmicb.2021.785318","volume":"12","author":"Q Yu","year":"2021","unstructured":"Yu Q, Li M, Liu M, Huang S, Wang G, Wang T et al (2021) Selection and characterization of SsDNA aptamers targeting largemouth bass virus infected cells with antiviral activities. Front Microbiol 12:785318","journal-title":"Front Microbiol"},{"issue":"3","key":"633_CR4","doi-asserted-by":"publisher","first-page":"e1785","DOI":"10.1002\/wnan.1785","volume":"14","author":"CKO Dzuvor","year":"2022","unstructured":"Dzuvor CKO, Tettey EL, Danquah MK (2022) Aptamers as promising nanotheranostic tools in the COVID-19 pandemic era. Wiley Interdiscip Rev Nanomed Nanobiotechnol 14(3):e1785","journal-title":"Wiley Interdiscip Rev Nanomed Nanobiotechnol"},{"key":"633_CR5","doi-asserted-by":"crossref","unstructured":"Hu C, Yang S, Li S, Liu X, Liu Y, Chen Z et al (2024) Viral aptamer screening and aptamer-based biosensors for virus detection: A review. Int J Biol Macromol. 133935","DOI":"10.1016\/j.ijbiomac.2024.133935"},{"key":"633_CR6","doi-asserted-by":"crossref","unstructured":"Chong C, Low C (2019) Synthetic antibody: prospects in aquaculture biosecurity. Fish Shellfish Immunol. 86","DOI":"10.1016\/j.fsi.2018.11.060"},{"issue":"7","key":"633_CR7","doi-asserted-by":"publisher","first-page":"622","DOI":"10.3390\/ph14070622","volume":"14","author":"A Kr\u00fcger","year":"2021","unstructured":"Kr\u00fcger A, de Jesus Santos AP, de S\u00e1 V, Ulrich H, Wrenger C (2021) Aptamer applications in emerging viral diseases. Pharmaceuticals 14(7):622","journal-title":"Pharmaceuticals"},{"key":"633_CR8","doi-asserted-by":"crossref","unstructured":"Zhang T, Lu Y, Deng S, Deng R (2021) Aptamers for the diagnosis of infectious diseases. Aptamers Med Appl Diagnosis Ther. 207\u2013238","DOI":"10.1007\/978-981-33-4838-7_8"},{"key":"633_CR9","doi-asserted-by":"publisher","first-page":"128677","DOI":"10.1016\/j.ijbiomac.2023.128677","volume":"257","author":"Z Chen","year":"2024","unstructured":"Chen Z, Sun Q, Yang Y, Nie X, Xiang W, Ren Y et al (2024) Aptamer-based diagnostic and therapeutic approaches for animal viruses: A review. Int J Biol Macromol 257:128677","journal-title":"Int J Biol Macromol"},{"issue":"2","key":"633_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/jfd.13892","volume":"47","author":"N Ghadin","year":"2024","unstructured":"Ghadin N, Yusof NAM, Syarul Nataqain B, Raston NHA, Low CF (2024) Selection and characterization of SsDNA aptamer targeting Macrobrachium rosenbergii nodavirus capsid protein: A potential capture agent in gold-nanoparticle-based aptasensor for viral protein detection. J Fish Dis 47(2):1\u201311","journal-title":"J Fish Dis"},{"key":"633_CR11","doi-asserted-by":"crossref","unstructured":"Ghadin N, Baharum SN, Ahmad Raston NH, Low C-F (2025) Truncation-Enhanced aptamer binding affinity and its potential as a sensor for Macrobrachium rosenbergii nodavirus detection. J Fish Dis. e14093","DOI":"10.1111\/jfd.14093"},{"key":"633_CR12","doi-asserted-by":"publisher","first-page":"713003","DOI":"10.3389\/fmolb.2021.713003","volume":"8","author":"F Cleri","year":"2021","unstructured":"Cleri F, Lensink MF, Blossey R (2021) DNA aptamers block the receptor binding domain at the Spike protein of SARS-CoV-2. Front Mol Biosci 8:713003","journal-title":"Front Mol Biosci"},{"issue":"18","key":"633_CR13","doi-asserted-by":"publisher","first-page":"10266","DOI":"10.1002\/anie.202100225","volume":"60","author":"M Sun","year":"2021","unstructured":"Sun M, Liu S, Wei X, Wan S, Huang M, Song T et al (2021) Aptamer blocking strategy inhibits SARS-CoV-2 virus infection. Angew Chemie Int Ed 60(18):10266\u201310272","journal-title":"Angew Chemie Int Ed"},{"key":"633_CR14","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","volume":"1","author":"MJ Abraham","year":"2015","unstructured":"Abraham MJ, Murtola T, Schulz R, P\u00e1ll S, Smith JC, Hess B et al (2015) GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1:19\u201325","journal-title":"SoftwareX"},{"issue":"16","key":"633_CR15","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1002\/jcc.20291","volume":"26","author":"D Van Der Spoel","year":"2005","unstructured":"Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005) GROMACS: fast, flexible, and free. J Comput Chem 26(16):1701\u20131718","journal-title":"J Comput Chem"},{"issue":"25","key":"633_CR16","doi-asserted-by":"publisher","first-page":"2135","DOI":"10.1002\/jcc.23354","volume":"34","author":"J Huang","year":"2013","unstructured":"Huang J, MacKerell AD Jr (2013) CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem 34(25):2135\u20132145","journal-title":"J Comput Chem"},{"issue":"11","key":"633_CR17","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.1002\/jcc.20945","volume":"29","author":"S Jo","year":"2008","unstructured":"Jo S, Kim T, Iyer VG, Im W (2008) CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem 29(11):1859\u20131865","journal-title":"J Comput Chem"},{"issue":"3","key":"633_CR18","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1021\/ct700301q","volume":"4","author":"B Hess","year":"2008","unstructured":"Hess B, Kutzner C, Van Der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4(3):435\u2013447","journal-title":"J Chem Theory Comput"},{"key":"633_CR19","doi-asserted-by":"crossref","unstructured":"Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys;126(1)","DOI":"10.1063\/1.2408420"},{"issue":"10","key":"633_CR20","doi-asserted-by":"publisher","first-page":"6281","DOI":"10.1021\/acs.jctc.1c00645","volume":"17","author":"MS Vald\u00e9s-Tresanco","year":"2021","unstructured":"Vald\u00e9s-Tresanco MS, Vald\u00e9s-Tresanco ME, Valiente PA, Moreno E (2021) gmx_MMPBSA: a new tool to perform end-state free energy calculations with GROMACS. J Chem Theory Comput 17(10):6281\u20136291","journal-title":"J Chem Theory Comput"},{"issue":"5","key":"633_CR21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/v14050945","volume":"14","author":"X Zhang","year":"2022","unstructured":"Zhang X, Zhang Z, Li J, Huang X, Wei J, Yang J et al (2022) A novel sandwich ELASA based on aptamer for detection of largemouth bass virus (LMBV). Viruses 14(5):1\u201310","journal-title":"Viruses"},{"issue":"41","key":"633_CR22","doi-asserted-by":"publisher","first-page":"23752","DOI":"10.1039\/C9RA02089F","volume":"9","author":"A Bosak","year":"2019","unstructured":"Bosak A, Saraf N, Willenberg A, Kwan MWC, Alto BW, Jackson GW et al (2019) Aptamer-gold nanoparticle conjugates for the colorimetric detection of arboviruses and vector mosquito species. RSC Adv 9(41):23752\u201323763","journal-title":"RSC Adv"},{"key":"633_CR23","doi-asserted-by":"publisher","first-page":"113768","DOI":"10.1016\/j.bios.2021.113768","volume":"197","author":"ATV Nguyen","year":"2022","unstructured":"Nguyen ATV, Duong BT, Park H, Yeo S-J (2022) Development of a peptide aptamer pair-linked rapid fluorescent diagnostic system for Zika virus detection. Biosens Bioelectron 197:113768","journal-title":"Biosens Bioelectron"},{"issue":"1","key":"633_CR24","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/s40580-022-00332-8","volume":"9","author":"G Park","year":"2022","unstructured":"Park G, Lee M, Kang J, Park C, Min J, Lee T (2022) Selection of DNA aptamer and its application as an electrical biosensor for Zika virus detection in human serum. Nano Converg 9(1):41","journal-title":"Nano Converg"},{"issue":"5","key":"633_CR25","first-page":"722","volume":"12","author":"R Thevendran","year":"2023","unstructured":"Thevendran R, Rogini S, Leighton G, Mutombwera A, Shigdar S, Tang T-H et al (2023) The diagnostic potential of RNA aptamers against the NS1 protein of dengue virus serotype 2. Biology (Basel) 12(5):722","journal-title":"Biology (Basel)"},{"key":"633_CR26","doi-asserted-by":"publisher","first-page":"e31473","DOI":"10.7554\/eLife.31473","volume":"7","author":"CJ Schlicksup","year":"2018","unstructured":"Schlicksup CJ, Wang JC-Y, Francis S, Venkatakrishnan B, Turner WW, VanNieuwenhze M et al (2018) Hepatitis B virus core protein allosteric modulators can distort and disrupt intact capsids. Elife 7:e31473","journal-title":"Elife"},{"issue":"23","key":"633_CR27","doi-asserted-by":"publisher","first-page":"e00840","DOI":"10.1128\/jvi.00840-22","volume":"96","author":"L Valiente","year":"2022","unstructured":"Valiente L, L\u00f3pez-Arg\u00fcello S, Rodr\\\u2019\\iguez-Huete A, Valbuena A, Mateu MG (2022) Molecular determinants of human rhinovirus infection, assembly, and conformational stability at capsid protein interfaces. J Virol 96(23):e00840\u2013e00822","journal-title":"J Virol"},{"issue":"42","key":"633_CR28","doi-asserted-by":"publisher","first-page":"28856","DOI":"10.1021\/jacs.4c08871","volume":"146","author":"R Kant","year":"2024","unstructured":"Kant R, Lee L-S, Patterson A, Gibes N, Venkatakrishnan B, Zlotnick A et al (2024) Small molecule assembly agonist alters the dynamics of hepatitis B virus core protein dimer and capsid. J Am Chem Soc 146(42):28856\u201328865","journal-title":"J Am Chem Soc"},{"key":"633_CR29","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1016\/j.antiviral.2016.02.009","volume":"129","author":"L Zhou","year":"2016","unstructured":"Zhou L, Li P, Yang M, Yu Y, Huang Y, Wei J et al (2016) Generation and characterization of novel DNA aptamers against coat protein of grouper nervous necrosis virus (GNNV) with antiviral activities and delivery potential in grouper cells. Antiviral Res 129:104\u2013114","journal-title":"Antiviral Res"},{"issue":"51","key":"633_CR30","doi-asserted-by":"publisher","first-page":"21541","DOI":"10.1021\/jacs.1c08226","volume":"143","author":"M Sun","year":"2021","unstructured":"Sun M, Liu S, Song T, Chen F, Zhang J, Huang J et al (2021) Spherical neutralizing aptamer inhibits SARS-CoV-2 infection and suppresses mutational escape. J Am Chem Soc 143(51):21541\u201321548","journal-title":"J Am Chem Soc"},{"key":"633_CR31","doi-asserted-by":"crossref","unstructured":"Torres-V\u00e1zquez B, de Lucas AM, Garc\\\u2019\\ia-Crespo C, Garc\\\u2019\\ia-Mart\\\u2019\\in JA, Fragoso A, Fern\u00e1ndez-Algar M et al (2022) In vitro selection of high affinity DNA and RNA aptamers that detect hepatitis C virus core protein of genotypes 1 to 4 and inhibit virus production in cell culture. J Mol Biol 167501","DOI":"10.1016\/j.jmb.2022.167501"},{"issue":"6","key":"633_CR32","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1002\/jcc.23973","volume":"37","author":"GR Bowman","year":"2016","unstructured":"Bowman GR (2016) Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation. J Comput Chem 37(6):558\u2013566","journal-title":"J Comput Chem"},{"key":"633_CR33","doi-asserted-by":"publisher","first-page":"595273","DOI":"10.3389\/fchem.2020.595273","volume":"8","author":"C Selvaraj","year":"2021","unstructured":"Selvaraj C, Panwar U, Dinesh DC, Boura E, Singh P, Dubey VK et al (2021) Microsecond MD simulation and multiple-conformation virtual screening to identify potential anti-COVID-19 inhibitors against SARS-CoV-2 main protease. Front Chem 8:595273","journal-title":"Front Chem"},{"issue":"21","key":"633_CR34","doi-asserted-by":"publisher","first-page":"10763","DOI":"10.1080\/07391102.2021.1948447","volume":"40","author":"P Kumar","year":"2022","unstructured":"Kumar P, Bhardwaj T, Kumar A, Garg N, Giri R (2022) One microsecond MD simulations of the SARS-CoV-2 main protease and hydroxychloroquine complex reveal the intricate nature of binding. J Biomol Struct Dyn 40(21):10763\u201310770","journal-title":"J Biomol Struct Dyn"},{"issue":"3","key":"633_CR35","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1093\/nar\/gkab1293","volume":"50","author":"PR Gruenke","year":"2022","unstructured":"Gruenke PR, Aneja R, Welbourn S, Ukah OB, Sarafianos SG, Burke DH et al (2022) Selection and identification of an RNA aptamer that specifically binds the HIV-1 capsid lattice and inhibits viral replication. Nucleic Acids Res 50(3):1701\u20131717","journal-title":"Nucleic Acids Res"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-025-00633-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10822-025-00633-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-025-00633-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T17:55:57Z","timestamp":1762451757000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10822-025-00633-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,23]]},"references-count":35,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,12]]}},"alternative-id":["633"],"URL":"https:\/\/doi.org\/10.1007\/s10822-025-00633-0","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"value":"0920-654X","type":"print"},{"value":"1573-4951","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,23]]},"assertion":[{"value":"14 April 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 July 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 July 2025","order":3,"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 competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"57"}}