{"id":"https://openalex.org/W4415216016","doi":"https://doi.org/10.1101/2025.10.15.682595","title":"Amyloid Explorer: a global atlas of amyloid fibril structures and thermodynamic principles","display_name":"Amyloid Explorer: a global atlas of amyloid fibril structures and thermodynamic principles","publication_year":2025,"publication_date":"2025-10-15","ids":{"openalex":"https://openalex.org/W4415216016","doi":"https://doi.org/10.1101/2025.10.15.682595"},"language":"en","primary_location":{"id":"doi:10.1101/2025.10.15.682595","doi":"https://doi.org/10.1101/2025.10.15.682595","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.10.15.682595","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/10/15/2025.10.15.682595.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2025/10/15/2025.10.15.682595.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5120011695","display_name":"Vasilis Kyriazis","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vasilis Kyriazis","raw_affiliation_strings":["UT Southwestern Medical Center;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UT Southwestern Medical Center;","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000183173","display_name":"Laxmikant G. Gadhe","orcid":"https://orcid.org/0000-0002-3157-2998","observed_orcids":["https://orcid.org/0000-0002-3157-2998"]},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laxmikant Gadhe","raw_affiliation_strings":["UT Southwestern Medical Center;"],"raw_orcid":"https://orcid.org/0000-0002-3157-2998","affiliations":[{"raw_affiliation_string":"UT Southwestern Medical Center;","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004765284","display_name":"Katerina Konstantoulea","orcid":"https://orcid.org/0000-0002-0960-6274","observed_orcids":["https://orcid.org/0000-0002-0960-6274"]},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katerina Konstantoulea","raw_affiliation_strings":["UT Southwestern Medical Center;"],"raw_orcid":"https://orcid.org/0000-0002-0960-6274","affiliations":[{"raw_affiliation_string":"UT Southwestern Medical Center;","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060221835","display_name":"Nikolaos N. Louros","orcid":"https://orcid.org/0000-0002-4030-1022","observed_orcids":["https://orcid.org/0000-0002-4030-1022"]},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nikolaos Louros","raw_affiliation_strings":["UT Southwestern Medical Center;"],"raw_orcid":"https://orcid.org/0000-0002-4030-1022","affiliations":[{"raw_affiliation_string":"UT Southwestern Medical Center;","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031589452","display_name":"Joost W. H. Schymkowitz","orcid":"https://orcid.org/0000-0003-2020-0168","observed_orcids":["https://orcid.org/0000-0003-2020-0168"]},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Joost Schymkowitz","raw_affiliation_strings":["KU Leuven"],"raw_orcid":"https://orcid.org/0000-0003-2020-0168","affiliations":[{"raw_affiliation_string":"KU Leuven","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008256216","display_name":"Fr\u00e9d\u00e9ric Rousseau","orcid":"https://orcid.org/0000-0002-9189-7399","observed_orcids":["https://orcid.org/0000-0002-9189-7399"]},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Frederic Rousseau","raw_affiliation_strings":["KU Leuven"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"KU Leuven","institution_ids":["https://openalex.org/I99464096"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5060221835"],"corresponding_institution_ids":["https://openalex.org/I867280407"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10086","display_name":"Alzheimer's disease research and treatments","score":0.5957000255584717,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10086","display_name":"Alzheimer's disease research and treatments","score":0.5957000255584717,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11335","display_name":"Prion Diseases and Protein Misfolding","score":0.18639999628067017,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.15379999577999115,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/amyloid-fibrils","display_name":"amyloid fibrils","score":0.9819999933242798},{"id":"https://openalex.org/keywords/protein-aggregation","display_name":"protein aggregation","score":0.5659999847412109}],"concepts":[{"id":"https://openalex.org/C2994168385","wikidata":"https://www.wikidata.org/wiki/Q6740853","display_name":"Amyloid fibril","level":4,"score":0.775600016117096},{"id":"https://openalex.org/C27523624","wikidata":"https://www.wikidata.org/wiki/Q14860849","display_name":"Fibril","level":2,"score":0.6309999823570251},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5242999792098999},{"id":"https://openalex.org/C2777633098","wikidata":"https://www.wikidata.org/wiki/Q2736051","display_name":"Amyloid (mycology)","level":2,"score":0.5188000202178955},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4406000077724457},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.40059998631477356},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3955000042915344},{"id":"https://openalex.org/C3019447875","wikidata":"https://www.wikidata.org/wiki/Q417667","display_name":"Amyloid \u03b2","level":3,"score":0.3953000009059906},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3797000050544739},{"id":"https://openalex.org/C2776673561","wikidata":"https://www.wikidata.org/wiki/Q655357","display_name":"Atlas (anatomy)","level":2,"score":0.37529999017715454},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.35530000925064087},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3395000100135803},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.3393999934196472},{"id":"https://openalex.org/C136238340","wikidata":"https://www.wikidata.org/wiki/Q7251455","display_name":"Protein aggregation","level":2,"score":0.33799999952316284},{"id":"https://openalex.org/C2909607560","wikidata":"https://www.wikidata.org/wiki/Q6740853","display_name":"Amyloid disease","level":5,"score":0.33340001106262207},{"id":"https://openalex.org/C2988375501","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein stability","level":2,"score":0.29910001158714294},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.2888000011444092},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.25859999656677246},{"id":"https://openalex.org/C180081513","wikidata":"https://www.wikidata.org/wiki/Q4914721","display_name":"Biochemistry of Alzheimer's disease","level":5,"score":0.2533000111579895}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/2025.10.15.682595","doi":"https://doi.org/10.1101/2025.10.15.682595","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.10.15.682595","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/10/15/2025.10.15.682595.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/2025.10.15.682595","doi":"https://doi.org/10.1101/2025.10.15.682595","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.10.15.682595","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/10/15/2025.10.15.682595.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2520931474","display_name":"The Hidden Biology of Inclusion Bodies","funder_award_id":"G0A6724N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G3110895200","display_name":null,"funder_award_id":"C0401","funder_id":"https://openalex.org/F4320322837","funder_display_name":"Vlaams Instituut voor Biotechnologie"}],"funders":[{"id":"https://openalex.org/F4320310169","display_name":"University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690"},{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320322837","display_name":"Vlaams Instituut voor Biotechnologie","ror":"https://ror.org/03xrhmk39"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null},{"id":"https://openalex.org/F4320331479","display_name":"Fondation pour la Recherche sur Alzheimer","ror":"https://ror.org/01z0nmr69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4415216016.pdf","grobid_xml":"https://content.openalex.org/works/W4415216016.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W1526832479","https://openalex.org/W2023490488","https://openalex.org/W2031239680","https://openalex.org/W2043338013","https://openalex.org/W2069152576","https://openalex.org/W2133425057","https://openalex.org/W2151581834","https://openalex.org/W2152562710","https://openalex.org/W2161072217","https://openalex.org/W2324362294","https://openalex.org/W2600803441","https://openalex.org/W2614053601","https://openalex.org/W2727929522","https://openalex.org/W2762906948","https://openalex.org/W2794954447","https://openalex.org/W2972174635","https://openalex.org/W2984696870","https://openalex.org/W3002616582","https://openalex.org/W3011713314","https://openalex.org/W3127304521","https://openalex.org/W3201122724","https://openalex.org/W3202815206","https://openalex.org/W3214964819","https://openalex.org/W4200102773","https://openalex.org/W4205867548","https://openalex.org/W4212808714","https://openalex.org/W4221035740","https://openalex.org/W4281287514","https://openalex.org/W4281664391","https://openalex.org/W4288052680","https://openalex.org/W4309410174","https://openalex.org/W4310945739","https://openalex.org/W4311840726","https://openalex.org/W4321071721","https://openalex.org/W4380886827","https://openalex.org/W4386532366","https://openalex.org/W4387107003","https://openalex.org/W4388934329","https://openalex.org/W4390937816","https://openalex.org/W4391509791","https://openalex.org/W4403044180","https://openalex.org/W4404797546","https://openalex.org/W4408073099","https://openalex.org/W4411193878","https://openalex.org/W4411900430","https://openalex.org/W4411932264","https://openalex.org/W4412699374","https://openalex.org/W4414824423","https://openalex.org/W4416334353"],"related_works":["https://openalex.org/W2050891813","https://openalex.org/W3181826210","https://openalex.org/W4412699374","https://openalex.org/W7135239275","https://openalex.org/W4407465790","https://openalex.org/W4281717300","https://openalex.org/W285250651","https://openalex.org/W1970435618","https://openalex.org/W7204033954","https://openalex.org/W3085581215"],"abstract_inverted_index":{"Amyloid":[0,43,113],"fibrils":[1],"underpin":[2],"both":[3],"functional":[4],"and":[5,9,37,58,66,73,104,127],"pathological":[6],"protein":[7,26],"assemblies":[8],"exhibit":[10],"extensive":[11],"structural":[12,70],"polymorphism.":[13],"More":[14],"than":[15],"600":[16],"high-resolution":[17],"fibril":[18,52],"structures":[19],"are":[20],"now":[21],"available":[22],"across":[23,79],"over":[24],"50":[25],"sequences,":[27],"yet":[28],"comparative":[29],"analysis":[30,78],"has":[31],"been":[32],"hindered":[33],"by":[34],"fragmented":[35],"resources":[36],"inconsistent":[38],"annotation.":[39],"Here":[40],"we":[41],"present":[42],"Explorer,":[44],"an":[45],"open-access":[46],"platform":[47,122],"that":[48],"integrates":[49],"the":[50,80,128],"complete":[51],"archive":[53,118],"into":[54,119],"a":[55,116,120],"standardized,":[56],"quality-controlled,":[57],"thermodynamically":[59],"annotated":[60],"framework.":[61],"Each":[62],"entry":[63],"includes":[64],"residue-":[65],"segment-level":[67],"stability":[68],"maps,":[69],"quality":[71],"metrics,":[72],"interactive":[74],"visualization":[75],"tools.":[76],"Global":[77],"dataset":[81],"reveals":[82],"conserved":[83,96],"rules":[84],"of":[85,95,130],"amyloid":[86],"assembly,":[87],"including":[88],"cooperative":[89],"cores,":[90],"framework":[91],"polymorphism":[92],"through":[93],"reuse":[94],"segments":[97],"in":[98],"distinct":[99],"folds,":[100],"polymorph-specific":[101],"energetic":[102],"anchors,":[103],"short":[105],"frustration":[106],"zones.":[107],"By":[108],"combining":[109],"scale":[110],"with":[111],"accessibility,":[112],"Explorer":[114],"transforms":[115],"static":[117],"discovery":[121],"for":[123],"mechanistic":[124],"insight,":[125],"classification,":[126],"design":[129],"aggregation":[131],"modulators.":[132]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-10-22T09:42:04.148104","created_date":"2025-10-16T00:00:00"}
