{"id":"https://openalex.org/W4415008273","doi":"https://doi.org/10.1021/acs.jcim.5c01241","title":"Multiscale Computational Workflow to Determine Stability of Disulfide Bridges in Proteins\u2500Application to IgG Antibodies","display_name":"Multiscale Computational Workflow to Determine Stability of Disulfide Bridges in Proteins\u2500Application to IgG Antibodies","publication_year":2025,"publication_date":"2025-10-09","ids":{"openalex":"https://openalex.org/W4415008273","doi":"https://doi.org/10.1021/acs.jcim.5c01241","pmid":"https://pubmed.ncbi.nlm.nih.gov/41066665"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c01241","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01241","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5060564303","display_name":"Saad S. M. Hassan","orcid":"https://orcid.org/0000-0001-6663-4565"},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sani Idris Alhassan","raw_affiliation_strings":["Institute of Physical Chemistry","Karlsruhe Institute of Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry","institution_ids":[]},{"raw_affiliation_string":"Karlsruhe Institute of Technology","institution_ids":["https://openalex.org/I102335020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025171662","display_name":"Tom\u00e1\u0161 Kuba\u0159","orcid":"https://orcid.org/0000-0002-2419-6912"},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Tom\u00e1\u0161 Kuba\u0159","raw_affiliation_strings":["Institute of Physical Chemistry","Karlsruhe Institute of Technology"],"raw_orcid":"https://orcid.org/0000-0002-2419-6912","affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry","institution_ids":[]},{"raw_affiliation_string":"Karlsruhe Institute of Technology","institution_ids":["https://openalex.org/I102335020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026196545","display_name":"Marcus Elstner","orcid":"https://orcid.org/0000-0002-3255-306X"},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marcus Elstner","raw_affiliation_strings":["Institute of Nanotechnology","Institute of Physical Chemistry","Karlsruhe Institute of Technology"],"raw_orcid":"https://orcid.org/0000-0002-3255-306X","affiliations":[{"raw_affiliation_string":"Institute of Nanotechnology","institution_ids":[]},{"raw_affiliation_string":"Institute of Physical Chemistry","institution_ids":[]},{"raw_affiliation_string":"Karlsruhe Institute of Technology","institution_ids":["https://openalex.org/I102335020"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009194232","display_name":"Julian B\u00f6ser","orcid":"https://orcid.org/0000-0001-9229-0700"},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Julian B\u00f6ser","raw_affiliation_strings":["Institute of Physical Chemistry","Karlsruhe Institute of Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physical Chemistry","institution_ids":[]},{"raw_affiliation_string":"Karlsruhe Institute of Technology","institution_ids":["https://openalex.org/I102335020"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5025171662"],"corresponding_institution_ids":["https://openalex.org/I102335020"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.32177711,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"65","issue":"20","first_page":"11187","last_page":"11202"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9994999766349792,"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":0.9973999857902527,"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/disulfide-bond","display_name":"Disulfide bond","score":0.7926999926567078},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.46239998936653137},{"id":"https://openalex.org/keywords/reduction","display_name":"Reduction (mathematics)","score":0.43970000743865967},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.4189000129699707},{"id":"https://openalex.org/keywords/monoclonal-antibody","display_name":"Monoclonal antibody","score":0.4041999876499176},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.4018999934196472},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.39910000562667847},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.39469999074935913},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.33799999952316284}],"concepts":[{"id":"https://openalex.org/C27256138","wikidata":"https://www.wikidata.org/wiki/Q1230226","display_name":"Disulfide bond","level":2,"score":0.7926999926567078},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5404000282287598},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.46239998936653137},{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.43970000743865967},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.4189000129699707},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.41269999742507935},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4099000096321106},{"id":"https://openalex.org/C542903549","wikidata":"https://www.wikidata.org/wiki/Q422248","display_name":"Monoclonal antibody","level":3,"score":0.4041999876499176},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.4018999934196472},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.39910000562667847},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.39469999074935913},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3837999999523163},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.33799999952316284},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3285999894142151},{"id":"https://openalex.org/C2780423959","wikidata":"https://www.wikidata.org/wiki/Q424257","display_name":"Molybdenum disulfide","level":2,"score":0.3257000148296356},{"id":"https://openalex.org/C4839761","wikidata":"https://www.wikidata.org/wiki/Q212111","display_name":"Spectral line","level":2,"score":0.3228999972343445},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.32030001282691956},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3160000145435333},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3111000061035156},{"id":"https://openalex.org/C155673373","wikidata":"https://www.wikidata.org/wiki/Q1648886","display_name":"Structural stability","level":2,"score":0.30869999527931213},{"id":"https://openalex.org/C135889238","wikidata":"https://www.wikidata.org/wiki/Q46276","display_name":"Kinetic energy","level":2,"score":0.29030001163482666},{"id":"https://openalex.org/C2988375501","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein stability","level":2,"score":0.2881999909877777},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.2879999876022339},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.2872999906539917},{"id":"https://openalex.org/C186399102","wikidata":"https://www.wikidata.org/wiki/Q903517","display_name":"Chemical stability","level":2,"score":0.2775000035762787},{"id":"https://openalex.org/C141123601","wikidata":"https://www.wikidata.org/wiki/Q6935072","display_name":"Multiscale modeling","level":2,"score":0.2727000117301941},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.26350000500679016},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.25920000672340393},{"id":"https://openalex.org/C2989164559","wikidata":"https://www.wikidata.org/wiki/Q15637420","display_name":"Low energy","level":2,"score":0.2549000084400177},{"id":"https://openalex.org/C14961307","wikidata":"https://www.wikidata.org/wiki/Q5377176","display_name":"Energy minimization","level":2,"score":0.2515999972820282},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.2513999938964844}],"mesh":[{"descriptor_ui":"D000069283","descriptor_name":"Rituximab","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000069283","descriptor_name":"Rituximab","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D007074","descriptor_name":"Immunoglobulin G","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D007074","descriptor_name":"Immunoglobulin G","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c01241","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01241","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:41066665","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41066665","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G402306430","display_name":null,"funder_award_id":"INST 40/575\u20101 FUGG","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G582076291","display_name":null,"funder_award_id":"GRK 2450","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321990","display_name":"Ministerium f\u00fcr Wissenschaft, Forschung und Kunst Baden-W\u00fcrttemberg","ror":"https://ror.org/01hc18p32"},{"id":"https://openalex.org/F4320325463","display_name":"Tertiary Education Trust Fund","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W804550063","https://openalex.org/W1031578623","https://openalex.org/W1555361166","https://openalex.org/W1666071927","https://openalex.org/W1891967301","https://openalex.org/W1968166922","https://openalex.org/W1975830725","https://openalex.org/W1979158821","https://openalex.org/W1989014138","https://openalex.org/W2000375213","https://openalex.org/W2004981238","https://openalex.org/W2005997381","https://openalex.org/W2012968301","https://openalex.org/W2017196167","https://openalex.org/W2018392691","https://openalex.org/W2023397454","https://openalex.org/W2030967651","https://openalex.org/W2040446474","https://openalex.org/W2047294350","https://openalex.org/W2051008192","https://openalex.org/W2057477511","https://openalex.org/W2058549653","https://openalex.org/W2059586921","https://openalex.org/W2061543226","https://openalex.org/W2062013025","https://openalex.org/W2065232574","https://openalex.org/W2069207490","https://openalex.org/W2093910582","https://openalex.org/W2096387523","https://openalex.org/W2109998627","https://openalex.org/W2116548552","https://openalex.org/W2139741311","https://openalex.org/W2141178114","https://openalex.org/W2141361924","https://openalex.org/W2144288821","https://openalex.org/W2146411229","https://openalex.org/W2149801992","https://openalex.org/W2161605421","https://openalex.org/W2161788422","https://openalex.org/W2164268395","https://openalex.org/W2168158378","https://openalex.org/W2323159942","https://openalex.org/W2327161550","https://openalex.org/W2563087913","https://openalex.org/W2587231831","https://openalex.org/W2592609622","https://openalex.org/W2746754830","https://openalex.org/W2986616908","https://openalex.org/W2989600197","https://openalex.org/W2993866869","https://openalex.org/W3013002235","https://openalex.org/W3023153122","https://openalex.org/W3153271966","https://openalex.org/W3214195467","https://openalex.org/W4206087165","https://openalex.org/W4206965603","https://openalex.org/W4211238896","https://openalex.org/W4297239791","https://openalex.org/W4382344269","https://openalex.org/W4389669976","https://openalex.org/W4391879799","https://openalex.org/W4403500106"],"related_works":[],"abstract_inverted_index":{"An":[0],"antibody":[1,37,125,165],"or":[2,28,126],"immunoglobulin":[3],"is":[4,82],"a":[5,54,123,156,163,167],"Y-shaped":[6],"assembly":[7],"of":[8,67,69,76,93,105,117,129,136,142,158,161],"four":[9],"peptide":[10],"chains,":[11],"stabilized":[12],"by":[13,97],"several":[14,130],"disulfide":[15,33,71,95,120,179],"bridges":[16,34,96,121,180],"that":[17],"are":[18,101,181],"critical":[19],"for":[20,89],"the":[21,36,41,60,70,74,77,90,94,115,118,127,134,147,153,159,177,187,193],"structure":[22,75],"and":[23,43,141,191],"function.":[24],"Failure":[25],"to":[26,31,39,58,113,184],"build":[27],"any":[29],"damage":[30],"these":[32],"makes":[35,110,146],"unable":[38],"assume":[40],"native":[42],"working":[44],"three-dimensional":[45],"structure.":[46],"Based":[47],"on":[48,84,155],"our":[49],"previous":[50],"developments,":[51],"we":[52],"present":[53],"multiscale":[55],"computational":[56,80],"framework":[57],"assess":[59],"thermodynamic":[61],"as":[62,64],"well":[63],"kinetic":[65],"stability":[66,160],"each":[68],"bonds":[72],"in":[73,103,173,195],"antibody.":[78],"The":[79],"strategy":[81],"based":[83],"generating":[85],"free":[86],"energy":[87,107],"surfaces":[88],"nonenzymatic":[91],"reduction":[92,185],"glutathione.":[98],"These":[99],"data":[100],"interpreted":[102],"terms":[104],"rate-limiting":[106],"barrier,":[108],"which":[109],"it":[111],"possible":[112],"compare":[114],"stabilities":[116,128],"different":[119,131],"within":[122],"single":[124],"antibodies.":[132],"Also,":[133],"application":[135],"efficient":[137],"quantum":[138],"chemistry":[139],"methods":[140,145],"enhanced":[143],"sampling":[144],"assessment":[148],"computationally":[149],"inexpensive.":[150],"We":[151,171],"showcase":[152],"method":[154],"study":[157],"rituximab,":[162],"monoclonal":[164],"with":[166],"widespread":[168],"clinical":[169],"use.":[170],"show":[172],"this":[174],"case":[175],"how":[176],"interchain":[178],"more":[182],"prone":[183],"than":[186],"intrachain":[188],"ones,":[189],"quantify":[190],"explain":[192],"differences":[194],"stability.":[196]},"counts_by_year":[],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
