{"id":"https://openalex.org/W7213916859","doi":"https://doi.org/10.5281/zenodo.22866148","title":"Reproducible code and supporting data for \"Developability-gated virtual screening of de novo anti-VEGF-A miniprotein binders\"","display_name":"Reproducible code and supporting data for \"Developability-gated virtual screening of de novo anti-VEGF-A miniprotein binders\"","publication_year":2026,"publication_date":"2026-09-21","ids":{"openalex":"https://openalex.org/W7213916859","doi":"https://doi.org/10.5281/zenodo.22866148"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.22866148","doi":"https://doi.org/10.5281/zenodo.22866148","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22866148","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,"listed_in":[],"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},"volume":null,"type":"software","is_traditional":false,"indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.22866148","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5152367181","display_name":"Sitao Yang","orcid":"https://orcid.org/0009-0006-6442-4250","observed_orcids":["https://orcid.org/0009-0006-6442-4250"]},"institutions":[{"id":"https://openalex.org/I6593398","display_name":"Dali University","ror":"https://ror.org/02y7rck89","country_code":"CN","type":"education","lineage":["https://openalex.org/I6593398"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yang, Sitao","raw_affiliation_strings":["The Third Affiliated Hospital of Dali University, Dali, Yunnan, China; College of Pharmacy, Dali University, Dali, Yunnan, China"],"raw_orcid":"https://orcid.org/0009-0006-6442-4250","affiliations":[{"raw_affiliation_string":"The Third Affiliated Hospital of Dali University, Dali, Yunnan, China; College of Pharmacy, Dali University, Dali, Yunnan, China","institution_ids":["https://openalex.org/I6593398"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5152367181"],"corresponding_institution_ids":["https://openalex.org/I6593398"],"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.7041000127792358,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.7041000127792358,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.18330000340938568,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.049300000071525574,"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/vegf-a","display_name":"VEGF-A","score":0.8199999928474426},{"id":"https://openalex.org/keywords/de-novo-protein-design","display_name":"de novo protein design","score":0.7390000224113464},{"id":"https://openalex.org/keywords/developability","display_name":"developability","score":0.6959999799728394},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"virtual screening","score":0.8730000257492065},{"id":"https://openalex.org/keywords/rfdiffusion","display_name":"RFdiffusion","score":0.671999990940094},{"id":"https://openalex.org/keywords/proteinmpnn","display_name":"ProteinMPNN","score":0.9190000295639038},{"id":"https://openalex.org/keywords/esmfold","display_name":"ESMFold","score":0.8090000152587891},{"id":"https://openalex.org/keywords/boltzmann-sampling","display_name":"Boltzmann sampling","score":0.6330000162124634},{"id":"https://openalex.org/keywords/mm-gbsa","display_name":"MM-GBSA","score":0.8659999966621399},{"id":"https://openalex.org/keywords/binding-affinity","display_name":"binding affinity","score":0.4690000116825104}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7106000185012817},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4916999936103821},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4544999897480011},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.43290001153945923},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.4172999858856201},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.398499995470047},{"id":"https://openalex.org/C158007255","wikidata":"https://www.wikidata.org/wiki/Q1055222","display_name":"Spectrum analyzer","level":2,"score":0.39640000462532043},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.3937999904155731},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.3418999910354614},{"id":"https://openalex.org/C146481406","wikidata":"https://www.wikidata.org/wiki/Q105131","display_name":"Hotspot (geology)","level":2,"score":0.33649998903274536},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.3357999920845032},{"id":"https://openalex.org/C47487241","wikidata":"https://www.wikidata.org/wiki/Q5227230","display_name":"Data access","level":2,"score":0.320499986410141},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.3050999939441681},{"id":"https://openalex.org/C3020493868","wikidata":"https://www.wikidata.org/wiki/Q55631277","display_name":"Real world data","level":2,"score":0.3025999963283539},{"id":"https://openalex.org/C171730128","wikidata":"https://www.wikidata.org/wiki/Q5227290","display_name":"Data file","level":2,"score":0.3012000024318695},{"id":"https://openalex.org/C188434589","wikidata":"https://www.wikidata.org/wiki/Q1478762","display_name":"Logic analyzer","level":3,"score":0.296099990606308},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.26759999990463257},{"id":"https://openalex.org/C2780977526","wikidata":"https://www.wikidata.org/wiki/Q42417149","display_name":"Data exploration","level":3,"score":0.26100000739097595},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.25529998540878296}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.5281/zenodo.22866148","doi":"https://doi.org/10.5281/zenodo.22866148","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22866148","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,"listed_in":[],"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},{"id":"doi:10.5281/zenodo.22866149","doi":"https://doi.org/10.5281/zenodo.22866149","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22866149","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,"listed_in":[],"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":"Software"},{"id":"doi:10.5281/zenodo.22866393","doi":"https://doi.org/10.5281/zenodo.22866393","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22866393","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,"listed_in":[],"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},{"id":"doi:10.5281/zenodo.22883914","doi":"https://doi.org/10.5281/zenodo.22883914","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22883914","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,"listed_in":[],"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},{"id":"doi:10.5281/zenodo.22886050","doi":"https://doi.org/10.5281/zenodo.22886050","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22886050","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,"listed_in":[],"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},{"id":"doi:10.5281/zenodo.23264354","doi":"https://doi.org/10.5281/zenodo.23264354","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23264354","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,"listed_in":[],"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"}],"best_oa_location":{"id":"doi:10.5281/zenodo.22866148","doi":"https://doi.org/10.5281/zenodo.22866148","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22866148","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,"listed_in":[],"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7213886798","https://openalex.org/W7213916370","https://openalex.org/W7108626812","https://openalex.org/W7145600031"],"abstract_inverted_index":{"Code":[0],"and":[1,42,85,93,114,119,137,153,180,205],"data":[2],"snapshot":[3],"for":[4,169,200],"the":[5,21,36,43,52,58,64,70,75,82,90,96,112,115,123,128,134,154,160,164,170,181,201,203],"manuscript":[6,54,165],"\"Developability-gated":[7],"virtual":[8],"screening":[9],"of":[10,31,88,217],"de":[11],"novo":[12],"anti-VEGF-A":[13],"miniprotein":[14],"binders\".":[15],"What":[16],"changed":[17],"in":[18,60,103,196],"v1.2":[19],"Corrected":[20,99],"author's":[22],"institutional":[23],"affiliation":[24],"to":[25],"its":[26],"official":[27],"English":[28],"name,":[29,77],"\"College":[30],"Pharmacy,":[32],"Dali":[33],"University\",":[34],"throughout":[35],"repository":[37,62],"(README,":[38],"LICENSE,":[39],"CODE_AUTHORS.md,":[40],"UPLOAD_GUIDE.md":[41],"script":[44],"headers).":[45],"Removed":[46],"a":[47],"stale":[48],"\",":[49],"multi-model\"":[50],"from":[51,95],"cited":[53],"title":[55,59],"so":[56,69],"that":[57],"this":[61],"matches":[63],"paper":[65],"verbatim.":[66],"Added":[67],".zenodo.json,":[68],"archived":[71],"record":[72,186],"now":[73],"carries":[74],"author":[76],"ORCID":[78],"(0009-0006-6442-4250),":[79],"both":[80,192],"affiliations,":[81],"MIT":[83,199],"licence":[84,94],"keywords":[86],"instead":[87],"inheriting":[89],"creator":[91],"name":[92],"GitHub":[97],"account.":[98],"two":[100],"documentation":[101],"errors":[102],"UPLOAD_GUIDE.md:":[104],"Zenodo":[105],"metadata":[106],"remains":[107],"editable":[108],"after":[109],"publication":[110],"(only":[111],"files":[113],"PID":[116],"are":[117,187,194,209],"immutable),":[118],"citations":[120],"should":[121],"use":[122],"version":[124],"DOI":[125,172],"rather":[126],"than":[127],"concept":[129],"DOI.":[130],"Contents":[131],"code/":[132],"-":[133,150,159],"design,":[135],"ranking":[136],"figure-generation":[138],"pipeline":[139],"(RFdiffusion":[140],"->":[141,143,145,147],"ProteinMPNN":[142],"ESMFold":[144],"Boltz-1":[146],"MM-GBSA).":[148],"data/":[149,208],"representative":[151],"structures":[152,206],"per-seed":[155],"energy":[156],"tables.":[157],"results/":[158],"derived":[161],"tables":[162,204],"behind":[163],"figures.":[166],"Repro":[167],"scripts":[168],"three-deposit":[171],"workflow":[173],"(zenodo_upload.py,":[174],"backfill_dois.py).":[175],"The":[176],"raw":[177],"model":[178],"outputs":[179],"APR-Score":[182],"/":[183],"CCS":[184],"recovery":[185],"deposited":[188],"separately":[189],"on":[190],"Zenodo;":[191],"DOIs":[193],"listed":[195],"results_manifest.md.":[197],"Licence:":[198],"code;":[202],"under":[207,211],"released":[210],"CC-BY-4.0.":[212],"Funding:":[213],"Yunnan":[214],"Provincial":[215],"Department":[216],"Education,":[218],"Grant":[219],"No.":[220],"2026J0890.":[221]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-09-22T00:00:00"}