{"id":"https://openalex.org/W7162132995","doi":"https://doi.org/10.48550/arxiv.2605.21600","title":"ConTact: Contact-First Antibody CDR Design via Explicit Interface Reasoning","display_name":"ConTact: Contact-First Antibody CDR Design via Explicit Interface Reasoning","publication_year":2026,"publication_date":"2026-05-20","ids":{"openalex":"https://openalex.org/W7162132995","doi":"https://doi.org/10.48550/arxiv.2605.21600"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.21600","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.21600","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2605.21600","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5136793122","display_name":"Mansoor Ahmed","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ahmed, Mansoor","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136760347","display_name":"Spencer VonBank","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"VonBank, Spencer","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136788469","display_name":"Nadeem Taj","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Taj, Nadeem","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136766896","display_name":"Sujin Lee","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lee, Sujin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136768315","display_name":"Naila Jan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jan, Naila","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5136723981","display_name":"Murray Patterson","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Patterson, Murray","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9369000196456909,"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":0.9369000196456909,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.04470000043511391,"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.003599999938160181,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/complementarity","display_name":"Complementarity (molecular biology)","score":0.5666000247001648},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4593000113964081},{"id":"https://openalex.org/keywords/prior-probability","display_name":"Prior probability","score":0.4115999937057495},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.3855000138282776},{"id":"https://openalex.org/keywords/signal","display_name":"SIGNAL (programming language)","score":0.3709999918937683},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.36899998784065247},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.321399986743927},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.3102000057697296}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6100000143051147},{"id":"https://openalex.org/C202269582","wikidata":"https://www.wikidata.org/wiki/Q2644277","display_name":"Complementarity (molecular biology)","level":2,"score":0.5666000247001648},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4593000113964081},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4496999979019165},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43860000371932983},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.4115999937057495},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.3855000138282776},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.3709999918937683},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.36899998784065247},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3398999869823456},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.321399986743927},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.3102000057697296},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.30709999799728394},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.3052000105381012},{"id":"https://openalex.org/C104267543","wikidata":"https://www.wikidata.org/wiki/Q208163","display_name":"Signal processing","level":3,"score":0.3010999858379364},{"id":"https://openalex.org/C2777508537","wikidata":"https://www.wikidata.org/wiki/Q7936620","display_name":"Visual reasoning","level":2,"score":0.29840001463890076},{"id":"https://openalex.org/C75553542","wikidata":"https://www.wikidata.org/wiki/Q178161","display_name":"A priori and a posteriori","level":2,"score":0.2937000095844269},{"id":"https://openalex.org/C190470478","wikidata":"https://www.wikidata.org/wiki/Q2370229","display_name":"Invariant (physics)","level":2,"score":0.26820001006126404},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.2556999921798706},{"id":"https://openalex.org/C85630698","wikidata":"https://www.wikidata.org/wiki/Q3826179","display_name":"Complementarity determining region","level":4,"score":0.2529999911785126}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.21600","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.21600","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2605.21600","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.21600","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Computational":[0],"antibody":[1],"CDR":[2,23,65],"design":[3,66,142],"methods":[4],"condition":[5],"on":[6,105],"antigen":[7,50,81],"structure":[8],"to":[9,40],"generate":[10],"binding":[11],"loops,":[12],"yet":[13],"existing":[14],"architectures":[15],"conflate":[16],"two":[17],"fundamentally":[18],"distinct":[19],"sub-problems:":[20],"identifying":[21],"which":[22],"positions":[24,54],"will":[25],"contact":[26,42],"the":[27,84,113,121],"antigen,":[28],"and":[29,78,133],"selecting":[30],"amino":[31],"acids":[32],"at":[33],"those":[34],"positions.":[35,107],"This":[36],"conflation":[37],"forces":[38],"models":[39],"learn":[41],"reasoning":[43],"implicitly":[44],"through":[45],"uniform":[46],"message":[47],"passing,":[48],"diluting":[49],"signal":[51,104],"across":[52],"all":[53],"equally.":[55],"We":[56],"introduce":[57],"ConTact,":[58],"a":[59,98],"contact-then-act":[60],"architecture":[61],"that":[62],"explicitly":[63],"decomposes":[64],"into":[67,83],"three":[68],"cascaded":[69],"stages:":[70],"learning":[71],"surface":[72],"complementarity":[73],"fingerprints,":[74],"predicting":[75],"CDR-antigen":[76],"contacts,":[77],"injecting":[79],"contact-gated":[80],"features":[82],"sequence":[85,135],"head.":[86],"A":[87],"distance-biased":[88],"cross-attention":[89],"module":[90],"encodes":[91],"geometric":[92],"priors":[93],"favoring":[94],"spatial":[95],"neighbors,":[96],"while":[97],"contact-weighted":[99],"cross-entropy":[100],"loss":[101],"concentrates":[102],"gradient":[103],"binding-critical":[106],"On":[108],"CHIMERA-Bench":[109],"dataset,":[110],"ConTact":[111],"achieves":[112],"best":[114,124],"structural":[115],"quality":[116],"(7%":[117],"RMSD":[118],"improvement":[119],"over":[120,130],"next-best":[122],"baseline),":[123],"epitope":[125],"awareness":[126],"(10%":[127],"F1":[128],"score":[129],"GNN":[131],"baselines),":[132],"competitive":[134],"recovery":[136],"(AAR":[137],"0.38)":[138],"among":[139],"several":[140],"CDR-H3":[141],"baselines.":[143]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2026-05-23T00:00:00"}