{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T08:49:00Z","timestamp":1780735740166,"version":"3.54.1"},"reference-count":29,"publisher":"Elsevier BV","issue":"6","license":[{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T00:00:00Z","timestamp":1684281600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000764","name":"King&apos;s College London","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000764","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001692","name":"Croucher Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001692","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017510","name":"UK Dementia Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100017510","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000288","name":"Royal Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports Methods"],"published-print":{"date-parts":[[2023,6]]},"DOI":"10.1016\/j.crmeth.2023.100499","type":"journal-article","created":{"date-parts":[[2023,6,12]],"date-time":"2023-06-12T10:40:05Z","timestamp":1686566405000},"page":"100499","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":14,"title":["A computational suite for the structural and functional characterization of amyloid aggregates"],"prefix":"10.1016","volume":"3","author":[{"given":"Zengjie","family":"Xia","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunzhao","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeff Yui Long","family":"Lam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziwei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melanie","family":"Burke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emre","family":"Fertan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rohan T.","family":"Ranasinghe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Hidari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John S.H.","family":"Danial","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Klenerman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.crmeth.2023.100499_bib2","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1038\/nature02261","article-title":"Protein folding and misfolding","volume":"426","author":"Dobson","year":"2003","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2023.100499_bib3","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1146\/annurev.biochem.75.101304.123901","article-title":"Protein misfolding, functional amyloid, and human disease","volume":"75","author":"Chiti","year":"2006","journal-title":"Annu. Rev. Biochem."},{"key":"10.1016\/j.crmeth.2023.100499_bib4","doi-asserted-by":"crossref","first-page":"1255555","DOI":"10.1126\/science.1255555","article-title":"Alzheimer\u2019s and Parkinson\u2019s diseases: the prion concept in relation to assembled A\u03b2, tau, and \u03b1-synuclein","volume":"349","author":"Goedert","year":"2015","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2023.100499_bib5","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/s41582-022-00642-9","article-title":"Lesions without symptoms: understanding resilience to Alzheimer disease neuropathological changes","volume":"18","author":"G\u00f3mez-Isla","year":"2022","journal-title":"Nat. Rev. Neurol."},{"key":"10.1016\/j.crmeth.2023.100499_bib6","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1126\/science.abm7285","article-title":"Cryo-EM structures of amyloid-\u03b2 42 filaments from human brains","volume":"375","author":"Yang","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2023.100499_bib7","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1038\/s41586-020-2317-6","article-title":"Structures of \u03b1-synuclein filaments from multiple system atrophy","volume":"585","author":"Schweighauser","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2023.100499_bib8","doi-asserted-by":"crossref","first-page":"7750","DOI":"10.1002\/anie.201700966","article-title":"Ultrasensitive measurement of Ca2+ influx into lipid vesicles induced by protein aggregates","volume":"56","author":"Flagmeier","year":"2017","journal-title":"Angew. Chem. Int. Ed."},{"key":"10.1016\/j.crmeth.2023.100499_bib9","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1021\/acschemneuro.5b00324","article-title":"Single-molecule imaging of individual amyloid protein aggregates in human biofluids","volume":"7","author":"Horrocks","year":"2016","journal-title":"ACS Chem. Neurosci."},{"key":"10.1016\/j.crmeth.2023.100499_bib10","doi-asserted-by":"crossref","first-page":"2033","DOI":"10.1002\/cbic.201800209","article-title":"Nanoscopic characterisation of individual endogenous protein aggregates in human neuronal cells","volume":"19","author":"Whiten","year":"2018","journal-title":"Chembiochem"},{"key":"10.1016\/j.crmeth.2023.100499_bib11","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1038\/nature10016","article-title":"Probing cellular protein complexes using single-molecule pull-down","volume":"473","author":"Jain","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2023.100499_bib12","doi-asserted-by":"crossref","first-page":"4756","DOI":"10.1021\/nl103427w","article-title":"Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami","volume":"10","author":"Jungmann","year":"2010","journal-title":"Nano Lett."},{"key":"10.1016\/j.crmeth.2023.100499_bib13","doi-asserted-by":"crossref","first-page":"fcab147","DOI":"10.1093\/braincomms\/fcab147","article-title":"Soluble amyloid beta-containing aggregates are present throughout the brain at early stages of Alzheimer\u2019s disease","volume":"3","author":"Sideris","year":"2021","journal-title":"Brain Commun."},{"key":"10.1016\/j.crmeth.2023.100499_bib14","doi-asserted-by":"crossref","first-page":"6172","DOI":"10.1002\/anie.200802376","article-title":"Subdiffraction-resolution fluorescence imaging with conventional fluorescent probes","volume":"47","author":"Heilemann","year":"2008","journal-title":"Angew. Chem. Int. Ed."},{"key":"10.1016\/j.crmeth.2023.100499_bib1","doi-asserted-by":"crossref","first-page":"1541","DOI":"10.1038\/s41467-019-09477-3","article-title":"Different soluble aggregates of A\u03b242 can give rise to cellular toxicity through different mechanisms","volume":"10","author":"De","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.crmeth.2023.100499_bib15","doi-asserted-by":"crossref","first-page":"5512","DOI":"10.1038\/s41467-022-33252-6","article-title":"Small soluble \u03b1-synuclein aggregates are the toxic species in Parkinson\u2019s disease","volume":"13","author":"Emin","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.crmeth.2023.100499_bib29","unstructured":"Katrukha E. 2020, ComDet plugin for ImageJ, v0.5.3, Zenodo, https:\/\/doi.org\/10.5281\/zenodo.4281064."},{"key":"10.1016\/j.crmeth.2023.100499_bib16","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.crmeth.2023.100499_bib17","doi-asserted-by":"crossref","first-page":"2389","DOI":"10.1093\/bioinformatics\/btu202","article-title":"ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging","volume":"30","author":"Ovesn\u00fd","year":"2014","journal-title":"Bioinforma. Oxf. Engl."},{"key":"10.1016\/j.crmeth.2023.100499_bib18","series-title":"aherbert\/gdsc-smlm: version 1.0","author":"Herbert","year":"2022"},{"key":"10.1016\/j.crmeth.2023.100499_bib19","series-title":"A Density-Based Algorithm for Discovering Clusters in Large Spatial Databases with Noise","first-page":"226","author":"Ester","year":"1996"},{"key":"10.1016\/j.crmeth.2023.100499_bib20","doi-asserted-by":"crossref","first-page":"3490","DOI":"10.1002\/1873-3468.13919","article-title":"Internalisation and toxicity of amyloid-\u03b2 1-42 are influenced by its conformation and assembly state rather than size","volume":"594","author":"Vadukul","year":"2020","journal-title":"FEBS Lett."},{"key":"10.1016\/j.crmeth.2023.100499_bib24","first-page":"e10","article-title":"Advanced methods of microscope control using \u03bcManager software","volume":"1","author":"Edelstein","year":"2014","journal-title":"J.\u00a0Biol. Methods"},{"key":"10.1016\/j.crmeth.2023.100499_bib28","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in Python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.crmeth.2023.100499_bib21","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1007\/s00401-019-02114-9","article-title":"PrP is a central player in toxicity mediated by soluble aggregates of neurodegeneration-causing proteins","volume":"139","author":"Corbett","year":"2020","journal-title":"Acta Neuropathol."},{"key":"10.1016\/j.crmeth.2023.100499_bib22","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/0896-6273(92)90117-V","article-title":"Tau proteins of alzheimer paired helical filaments: abnormal phosphorylation of all six brain isoforms","volume":"8","author":"Goedert","year":"1992","journal-title":"Neuron"},{"key":"10.1016\/j.crmeth.2023.100499_bib23","article-title":"An economic, square-shaped flat-field illumination module for TIRF-based super-resolution microscopy","author":"Lam","year":"2021","journal-title":"bioRxiv"},{"key":"10.1016\/j.crmeth.2023.100499_bib25","doi-asserted-by":"crossref","DOI":"10.3791\/50549-v","article-title":"Surface passivation for single-molecule protein studies","author":"Chandradoss","year":"2014","journal-title":"J.\u00a0Vis. Exp."},{"key":"10.1016\/j.crmeth.2023.100499_bib26","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1038\/nprot.2011.452","article-title":"Single-molecule pull-down for studying protein interactions","volume":"7","author":"Jain","year":"2012","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.crmeth.2023.100499_bib27","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1038\/s41557-020-0506-4","article-title":"Single-molecule visualization of DNA G-quadruplex formation in live cells","volume":"12","author":"Di Antonio","year":"2020","journal-title":"Nat. Chem."}],"container-title":["Cell Reports Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237523001285?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237523001285?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T22:59:39Z","timestamp":1762642779000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2667237523001285"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6]]},"references-count":29,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,6]]}},"alternative-id":["S2667237523001285"],"URL":"https:\/\/doi.org\/10.1016\/j.crmeth.2023.100499","relation":{},"ISSN":["2667-2375"],"issn-type":[{"value":"2667-2375","type":"print"}],"subject":[],"published":{"date-parts":[[2023,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A computational suite for the structural and functional characterization of amyloid aggregates","name":"articletitle","label":"Article Title"},{"value":"Cell Reports Methods","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.crmeth.2023.100499","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Authors.","name":"copyright","label":"Copyright"}],"article-number":"100499"}}