{"id":"https://openalex.org/W2381451619","doi":"https://doi.org/10.1017/s0263574716000199","title":"Influence of model resolution on geometric simulations of antibody aggregation","display_name":"Influence of model resolution on geometric simulations of antibody aggregation","publication_year":2016,"publication_date":"2016-05-13","ids":{"openalex":"https://openalex.org/W2381451619","doi":"https://doi.org/10.1017/s0263574716000199","mag":"2381451619"},"language":"en","primary_location":{"id":"doi:10.1017/s0263574716000199","is_oa":false,"landing_page_url":"https://doi.org/10.1017/s0263574716000199","pdf_url":null,"source":{"id":"https://openalex.org/S92163612","display_name":"Robotica","issn_l":"0263-5747","issn":["0263-5747","1469-8668"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311721","host_organization_name":"Cambridge University Press","host_organization_lineage":["https://openalex.org/P4310311721","https://openalex.org/P4310311702"],"host_organization_lineage_names":["Cambridge University Press","University of Cambridge"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Robotica","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079697685","display_name":"Kasra Manavi","orcid":null},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kasra Manavi","raw_affiliation_strings":["Department of Computer Science, University of New Mexico, 87131 Albuquerque, New Mexico. Emails:","Department of Computer Science,University of New Mexico,87131 Albuquerque,New Mexico. Emails:kazaz@cs.unm.edu,bjacobson@cs.unm.edu,bhoard@cs.unm.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of New Mexico, 87131 Albuquerque, New Mexico. Emails:","institution_ids":["https://openalex.org/I169521973"]},{"raw_affiliation_string":"Department of Computer Science,University of New Mexico,87131 Albuquerque,New Mexico. Emails:kazaz@cs.unm.edu,bjacobson@cs.unm.edu,bhoard@cs.unm.edu","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024549284","display_name":"Bruna Jacobson","orcid":"https://orcid.org/0000-0001-7718-9794"},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bruna Jacobson","raw_affiliation_strings":["Department of Computer Science, University of New Mexico, 87131 Albuquerque, New Mexico. Emails:","Department of Computer Science,University of New Mexico,87131 Albuquerque,New Mexico. Emails:kazaz@cs.unm.edu,bjacobson@cs.unm.edu,bhoard@cs.unm.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of New Mexico, 87131 Albuquerque, New Mexico. Emails:","institution_ids":["https://openalex.org/I169521973"]},{"raw_affiliation_string":"Department of Computer Science,University of New Mexico,87131 Albuquerque,New Mexico. Emails:kazaz@cs.unm.edu,bjacobson@cs.unm.edu,bhoard@cs.unm.edu","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054293772","display_name":"Brittany R. Hoard","orcid":"https://orcid.org/0000-0002-1897-1388"},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brittany Hoard","raw_affiliation_strings":["Department of Computer Science, University of New Mexico, 87131 Albuquerque, New Mexico. Emails:","Department of Computer Science,University of New Mexico,87131 Albuquerque,New Mexico. Emails:kazaz@cs.unm.edu,bjacobson@cs.unm.edu,bhoard@cs.unm.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of New Mexico, 87131 Albuquerque, New Mexico. Emails:","institution_ids":["https://openalex.org/I169521973"]},{"raw_affiliation_string":"Department of Computer Science,University of New Mexico,87131 Albuquerque,New Mexico. Emails:kazaz@cs.unm.edu,bjacobson@cs.unm.edu,bhoard@cs.unm.edu","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060753774","display_name":"Lydia Tapia","orcid":"https://orcid.org/0000-0002-7822-7091"},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lydia Tapia","raw_affiliation_strings":["Department of Computer Science, University of New Mexico, 87131 Albuquerque, New Mexico. Emails:","Department of Computer Science,University of New Mexico,87131 Albuquerque,New Mexico. Emails:kazaz@cs.unm.edu,bjacobson@cs.unm.edu,bhoard@cs.unm.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of New Mexico, 87131 Albuquerque, New Mexico. Emails:","institution_ids":["https://openalex.org/I169521973"]},{"raw_affiliation_string":"Department of Computer Science,University of New Mexico,87131 Albuquerque,New Mexico. Emails:kazaz@cs.unm.edu,bjacobson@cs.unm.edu,bhoard@cs.unm.edu","institution_ids":["https://openalex.org/I169521973"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5060753774"],"corresponding_institution_ids":["https://openalex.org/I169521973"],"apc_list":null,"apc_paid":null,"fwci":1.3022,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.79457985,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"34","issue":"8","first_page":"1754","last_page":"1776"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"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/T11124","display_name":"Protein purification and stability","score":0.9983999729156494,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9958000183105469,"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/degranulation","display_name":"Degranulation","score":0.6708940267562866},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.5278561115264893},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.466654509305954},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.43247249722480774},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4101994037628174},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3812139332294464},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3731768727302551},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.31939083337783813},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2188614010810852},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.17299684882164001},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.10446199774742126}],"concepts":[{"id":"https://openalex.org/C49802076","wikidata":"https://www.wikidata.org/wiki/Q5251810","display_name":"Degranulation","level":3,"score":0.6708940267562866},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.5278561115264893},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.466654509305954},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.43247249722480774},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4101994037628174},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3812139332294464},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3731768727302551},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.31939083337783813},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2188614010810852},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.17299684882164001},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.10446199774742126},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1017/s0263574716000199","is_oa":false,"landing_page_url":"https://doi.org/10.1017/s0263574716000199","pdf_url":null,"source":{"id":"https://openalex.org/S92163612","display_name":"Robotica","issn_l":"0263-5747","issn":["0263-5747","1469-8668"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311721","host_organization_name":"Cambridge University Press","host_organization_lineage":["https://openalex.org/P4310311721","https://openalex.org/P4310311702"],"host_organization_lineage_names":["Cambridge University Press","University of Cambridge"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Robotica","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310632","display_name":"Center for Evolutionary and Theoretical Immunology","ror":"https://ror.org/05fs6jp91"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320338304","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W137961148","https://openalex.org/W1555718279","https://openalex.org/W1832276623","https://openalex.org/W1969112250","https://openalex.org/W1973846182","https://openalex.org/W1974462994","https://openalex.org/W1979063761","https://openalex.org/W1981436290","https://openalex.org/W1986649132","https://openalex.org/W1987922325","https://openalex.org/W1994344551","https://openalex.org/W1996196145","https://openalex.org/W1996819948","https://openalex.org/W1999583932","https://openalex.org/W1999958724","https://openalex.org/W2004732798","https://openalex.org/W2015526636","https://openalex.org/W2018783142","https://openalex.org/W2023568310","https://openalex.org/W2027926022","https://openalex.org/W2036238089","https://openalex.org/W2040882581","https://openalex.org/W2047331390","https://openalex.org/W2051757997","https://openalex.org/W2052558212","https://openalex.org/W2067634728","https://openalex.org/W2067763399","https://openalex.org/W2075987376","https://openalex.org/W2076270456","https://openalex.org/W2079704365","https://openalex.org/W2084631697","https://openalex.org/W2086376468","https://openalex.org/W2086679183","https://openalex.org/W2086928685","https://openalex.org/W2087148323","https://openalex.org/W2090357311","https://openalex.org/W2091734240","https://openalex.org/W2098055048","https://openalex.org/W2102968948","https://openalex.org/W2113994268","https://openalex.org/W2118649335","https://openalex.org/W2124885315","https://openalex.org/W2135158074","https://openalex.org/W2136558879","https://openalex.org/W2142532813","https://openalex.org/W2146773519","https://openalex.org/W2158550010","https://openalex.org/W2158603948","https://openalex.org/W2163493106","https://openalex.org/W2165714871","https://openalex.org/W2168518560","https://openalex.org/W2170780924","https://openalex.org/W2171624654","https://openalex.org/W2172159758","https://openalex.org/W2315703236","https://openalex.org/W2324559726","https://openalex.org/W2324665896","https://openalex.org/W2326996508","https://openalex.org/W2414895359","https://openalex.org/W2518329001","https://openalex.org/W4313333784"],"related_works":["https://openalex.org/W2013608203","https://openalex.org/W2981295279","https://openalex.org/W3143557570","https://openalex.org/W2007728595","https://openalex.org/W2368476846","https://openalex.org/W4313368904","https://openalex.org/W4380225013","https://openalex.org/W4313382967","https://openalex.org/W2412307814","https://openalex.org/W2414745257"],"abstract_inverted_index":{"SUMMARY":[0],"It":[1],"is":[2,19,176,204],"estimated":[3],"that":[4,200],"allergies":[5,18],"afflict":[6],"up":[7],"to":[8,28,77],"40%":[9],"of":[10,22,37,61,100,127,132,147,202,252],"the":[11,20,57,69,95,125,155,162,229],"world's":[12],"population.":[13],"A":[14],"primary":[15],"mediator":[16],"for":[17,206],"aggregation":[21,84],"antigens":[23],"and":[24,40,45,59,81,98,116,143,161,189],"IgE":[25],"antibodies":[26],"bound":[27],"cell-surface":[29],"receptors,":[30],"Fc\u03b5RI.":[31],"Antibody/antigen":[32],"aggregate":[33],"formation":[34],"causes":[35],"stimulation":[36],"mast":[38],"cells":[39],"basophils,":[41],"initiating":[42],"cellular":[43],"degranulation":[44],"releasing":[46],"immune":[47],"mediators":[48],"which":[49,238],"produce":[50],"an":[51,106],"allergic":[52,70],"or":[53],"anaphylactic":[54],"response.":[55,71],"Understanding":[56],"shape":[58],"structure":[60],"these":[62],"aggregates":[63],"can":[64,171,239],"provide":[65],"critical":[66],"insights":[67],"into":[68],"We":[72,198],"have":[73],"previously":[74,138],"developed":[75,139],"methods":[76,151],"geometrically":[78],"model,":[79],"simulate":[80],"analyze":[82],"antibody":[83],"inspired":[85],"by":[86,228],"rigid":[87],"body":[88],"robotic":[89],"motion":[90],"simulations.":[91],"Our":[92,174],"technique":[93],"handles":[94],"large":[96],"size":[97],"number":[99],"molecules":[101],"involved":[102],"in":[103,231,266],"aggregation,":[104],"providing":[105,157,164],"advantage":[107],"over":[108],"traditional":[109],"simulations":[110,131],"such":[111],"as":[112],"molecular":[113],"dynamics":[114],"(MD)":[115],"coarse-grained":[117],"energetic":[118],"models.":[119],"In":[120],"this":[121],"paper,":[122],"we":[123],"study":[124],"impact":[126,201,216],"model":[128,245],"resolution":[129,203,232],"on":[130,178,217],"geometric":[133,159,248],"structures":[134],"using":[135,242],"both":[136],"our":[137,253],"Monte":[140],"Carlo":[141],"simulation":[142,254],"a":[144,165,181,190,196,208,214,219,221,243],"novel":[145],"application":[146],"rule-based":[148,244],"modeling.":[149],"These":[150],"complement":[152],"each":[153],"other,":[154],"former":[156],"explicit":[158],"detail":[160],"latter":[163],"generic":[166],"representation":[167],"where":[168],"multiple":[169],"resolutions":[170],"be":[172,240],"captured.":[173],"exploration":[175],"focused":[177],"two":[179],"antigens,":[180],"man-made":[182],"antigen":[183],"with":[184,246,260],"three":[185],"binding":[186,235],"sites,":[187],"DF3,":[188,207],"common":[191],"shrimp":[192],"allergen":[193],"(antigen),":[194],"Pen":[195,218],"1.":[197],"find":[199],"minimal":[205],"small":[209],"globular":[210],"antigen,":[211],"but":[212],"has":[213],"larger":[215],"1,":[220],"rod-shaped":[222],"molecule.":[223],"The":[224],"volume":[225],"reduction":[226],"caused":[227],"loss":[230],"allows":[233],"more":[234],"site":[236],"accessibility,":[237],"quantified":[241],"implicit":[247],"input.":[249],"Clustering":[250],"analysis":[251],"shows":[255],"good":[256],"correlation":[257],"when":[258],"compared":[259],"available":[261],"experimental":[262],"results.":[263],"Moreover,":[264],"collisions":[265],"all-atom":[267],"reconstructions":[268],"are":[269],"negligible,":[270],"at":[271,274],"around":[272],"0.2%":[273],"90%":[275],"reduction.":[276]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
