{"id":"https://openalex.org/W6968112985","doi":"https://doi.org/10.5281/zenodo.15331309","title":"Virtual Lab Data","display_name":"Virtual Lab Data","publication_year":2025,"publication_date":"2025-05-03","ids":{"openalex":"https://openalex.org/W6968112985","doi":"https://doi.org/10.5281/zenodo.15331309"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.15331309","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.15331309","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"dataset"},"type":"dataset","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.15331309","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Swanson, Kyle","orcid":"https://orcid.org/0000-0002-7385-7844"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Swanson, Kyle","raw_affiliation_strings":["Stanford University"],"affiliations":[{"raw_affiliation_string":"Stanford University","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Wu, Wesley","orcid":"https://orcid.org/0000-0003-4594-0699"},"institutions":[{"id":"https://openalex.org/I4210121800","display_name":"Chan Zuckerberg Initiative (United States)","ror":"https://ror.org/02qenvm24","country_code":"US","type":"company","lineage":["https://openalex.org/I4210121800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wu, Wesley","raw_affiliation_strings":["Chan Zuckerberg Biohub San Francisco"],"affiliations":[{"raw_affiliation_string":"Chan Zuckerberg Biohub San Francisco","institution_ids":["https://openalex.org/I4210121800"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Bulaong, Nash","orcid":null},"institutions":[{"id":"https://openalex.org/I4210121800","display_name":"Chan Zuckerberg Initiative (United States)","ror":"https://ror.org/02qenvm24","country_code":"US","type":"company","lineage":["https://openalex.org/I4210121800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bulaong, Nash","raw_affiliation_strings":["Chan Zuckerberg Biohub San Francisco"],"affiliations":[{"raw_affiliation_string":"Chan Zuckerberg Biohub San Francisco","institution_ids":["https://openalex.org/I4210121800"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Pak, John","orcid":"https://orcid.org/0000-0002-2998-9735"},"institutions":[{"id":"https://openalex.org/I4210121800","display_name":"Chan Zuckerberg Initiative (United States)","ror":"https://ror.org/02qenvm24","country_code":"US","type":"company","lineage":["https://openalex.org/I4210121800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pak, John","raw_affiliation_strings":["Chan Zuckerberg Biohub San Francisco"],"affiliations":[{"raw_affiliation_string":"Chan Zuckerberg Biohub San Francisco","institution_ids":["https://openalex.org/I4210121800"]}]},{"author_position":"last","author":{"id":null,"display_name":"Zou, James","orcid":"https://orcid.org/0000-0001-8880-4764"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zou, James","raw_affiliation_strings":["Stanford University"],"affiliations":[{"raw_affiliation_string":"Stanford University","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"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":true,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6642000079154968},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5501999855041504},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.48080000281333923},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.47119998931884766},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.44620001316070557},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.3594000041484833},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.35850000381469727}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6661999821662903},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6642000079154968},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5501999855041504},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.48080000281333923},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.47119998931884766},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.44620001316070557},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3790999948978424},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.3594000041484833},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.35850000381469727},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.3580999970436096},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.35749998688697815},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.35580000281333923},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3172999918460846},{"id":"https://openalex.org/C25344961","wikidata":"https://www.wikidata.org/wiki/Q192726","display_name":"Virtual machine","level":2,"score":0.3043999969959259},{"id":"https://openalex.org/C2777609615","wikidata":"https://www.wikidata.org/wiki/Q2527919","display_name":"Virtual Laboratory","level":2,"score":0.272599995136261},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.26579999923706055},{"id":"https://openalex.org/C2778022156","wikidata":"https://www.wikidata.org/wiki/Q576145","display_name":"Strain (injury)","level":2,"score":0.2590999901294708},{"id":"https://openalex.org/C58861120","wikidata":"https://www.wikidata.org/wiki/Q1330734","display_name":"Virtual file system","level":5,"score":0.25870001316070557}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5281/zenodo.15331309","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.15331309","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"dataset"}],"best_oa_location":{"id":"doi:10.5281/zenodo.15331309","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.15331309","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"dataset"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Data":[0],"for":[1,21,33,182],"the":[2,28,34,38,51,56,62,82,88,92,100,108,115,129,142,154,160,165,172],"Virtual":[3,10,39,63],"Lab.":[4,64],"Please":[5],"see":[6],"our":[7],"paper":[8],"The":[9,24,46],"Lab:":[11],"AI":[12],"Agents":[13],"Design":[14],"New":[15],"SARS-CoV-2":[16],"Nanobodies":[17],"with":[18,178],"Experimental":[19],"Validation":[20],"more":[22],"details.":[23],"file":[25,47],"ELISA_data_RBDs_nanobodies.xlsx":[26],"contains":[27,50,107,159,171],"experimental":[29,183],"ELISA":[30],"binding":[31,80,84],"data":[32],"nanobodies":[35,119],"designed":[36],"by":[37,61],"Lab":[40],"and":[41,73,111,123,137,145],"several":[42],"variants":[43],"of":[44,54,69,87,91,95,99,132],"SARS-CoV-2.":[45,96,133],"called":[48],"\"designed.zip\"":[49],"computational":[52],"results":[53,113,147],"running":[55,70],"nanobody":[57],"design":[58],"pipeline":[59],"created":[60],"This":[65,105,157,169],"involves":[66],"iterative":[67],"rounds":[68],"ESM,":[71,109,143],"AlphaFold-Multimer,":[72,110,144],"Rosetta":[74,112,146],"to":[75,81,128],"identify":[76],"mutations":[77,152],"that":[78],"optimize":[79],"receptor":[83],"domain":[85],"(RBD)":[86],"spike":[89],"protein":[90],"KP.3":[93],"variant":[94],"A":[97],"summary":[98],"contents":[101],"is":[102],"below.":[103],"round_0:":[104],"folder":[106,158,170],"on":[114],"four":[116,151,166],"starting":[117],"wild-type":[118],"Ty1,":[120],"Nb21,":[121],"H11-D4,":[122],"VHH-72,":[124],"which":[125],"all":[126],"bind":[127],"Wuhan":[130],"strain":[131],"round_1,":[134],"round_2,":[135],"round_3,":[136],"round_4:":[138],"These":[139],"folders":[140],"contain":[141],"after":[148],"iteratively":[149],"introducing":[150],"into":[153],"nanobodies.":[155],"selected:":[156],"top":[161,174],"mutant":[162,175],"sequences":[163,176],"across":[164],"rounds.":[167],"combined:":[168],"same":[173],"but":[177],"additional":[179],"sequence":[180],"tags":[181],"validation.":[184]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2025-11-06T06:51:31.235846","created_date":"2025-10-10T00:00:00"}
