{"id":"https://openalex.org/W7157146645","doi":"https://doi.org/10.48550/arxiv.2604.22800","title":"RCSB PDB AI Help Desk: retrieval-augmented generation for protein structure deposition support","display_name":"RCSB PDB AI Help Desk: retrieval-augmented generation for protein structure deposition support","publication_year":2026,"publication_date":"2026-04-13","ids":{"openalex":"https://openalex.org/W7157146645","doi":"https://doi.org/10.48550/arxiv.2604.22800"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2604.22800","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.22800","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2604.22800","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114852256","display_name":"Vivek Reddy Chithari","orcid":null},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chithari, Vivek Reddy","raw_affiliation_strings":["RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5134767598","display_name":"Jasmine Y. Young","orcid":null},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Young, Jasmine Y.","raw_affiliation_strings":["RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049398910","display_name":"Irina Persikova","orcid":"https://orcid.org/0000-0001-9544-8390"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Persikova, Irina","raw_affiliation_strings":["RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133546816","display_name":"Yuhe Liang","orcid":null},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liang, Yuhe","raw_affiliation_strings":["RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133526336","display_name":"Gregg V. Crichlow","orcid":null},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Crichlow, Gregg V.","raw_affiliation_strings":["RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010236766","display_name":"Justin W. Flatt","orcid":"https://orcid.org/0000-0001-5406-8156"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Flatt, Justin W.","raw_affiliation_strings":["RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002125253","display_name":"Sutapa Ghosh","orcid":"https://orcid.org/0000-0001-8784-0894"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ghosh, Sutapa","raw_affiliation_strings":["RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015493418","display_name":"Brian P. Hudson","orcid":"https://orcid.org/0000-0001-6121-9442"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hudson, Brian P.","raw_affiliation_strings":["RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003071304","display_name":"Ezra Peisach","orcid":"https://orcid.org/0000-0002-7905-6327"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peisach, Ezra","raw_affiliation_strings":["RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074598075","display_name":"Monica Sekharan","orcid":"https://orcid.org/0000-0002-2694-7003"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sekharan, Monica","raw_affiliation_strings":["RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048277979","display_name":"Chenghua Shao","orcid":"https://orcid.org/0000-0001-6817-7476"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shao, Chenghua","raw_affiliation_strings":["RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5132834656","display_name":"Stephen K. Burley","orcid":null},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Burley, Stephen K.","raw_affiliation_strings":["RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ, USA","institution_ids":["https://openalex.org/I102322142"]},{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, CA, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.4652000069618225,"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"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.4652000069618225,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.09139999747276306,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.052299998700618744,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.8324999809265137},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.6093000173568726},{"id":"https://openalex.org/keywords/desk","display_name":"Desk","score":0.6043999791145325},{"id":"https://openalex.org/keywords/fingerprint","display_name":"Fingerprint (computing)","score":0.4068000018596649},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.40639999508857727}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.8324999809265137},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.6093000173568726},{"id":"https://openalex.org/C2776545233","wikidata":"https://www.wikidata.org/wiki/Q1064858","display_name":"Desk","level":2,"score":0.6043999791145325},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5515999794006348},{"id":"https://openalex.org/C2777826928","wikidata":"https://www.wikidata.org/wiki/Q3745713","display_name":"Fingerprint (computing)","level":2,"score":0.4068000018596649},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.40639999508857727},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4052000045776367},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.376800000667572},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.34540000557899475},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2565999925136566},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.2517000138759613}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2604.22800","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.22800","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2604.22800","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.22800","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"Preprint"},"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":{"Motivation:":[0],"Structural":[1],"Biologists":[2],"have":[3],"contributed":[4],"more":[5,39],"than":[6,40],"245,000":[7],"experimentally":[8],"determined":[9],"three-dimensional":[10],"structures":[11],"of":[12,42,118],"biological":[13],"macromolecules":[14],"to":[15],"the":[16,32],"Protein":[17],"Data":[18],"Bank":[19],"(PDB).":[20],"Incoming":[21],"data":[22],"are":[23],"validated":[24],"and":[25,86,110,131,152],"biocurated":[26],"by":[27],"~20":[28],"expert":[29],"biocurators":[30,36],"across":[31],"wwPDB.":[33],"RCSB":[34],"PDB":[35],"who":[37],"process":[38],"40%":[41],"global":[43],"depositions":[44],"face":[45],"increasing":[46],"challenges":[47],"in":[48,58,65,135],"maintaining":[49],"efficient":[50],"Help":[51,72],"Desk":[52,73],"operations,":[53],"with":[54,81,139,147],"approximately":[55,59],"19,000":[56],"messages":[57],"8,000":[60],"entries":[61],"received":[62],"from":[63],"depositors":[64],"2025.":[66],"Results:":[67],"We":[68],"developed":[69],"an":[70],"AI-powered":[71],"using":[74],"Retrieval-Augmented":[75],"Generation":[76],"(RAG)":[77],"built":[78],"on":[79,137],"LangChain":[80],"a":[82,103,111],"pgvector":[83],"store":[84],"(PostgreSQL)":[85],"GPT-4.1-mini.":[87],"The":[88],"system":[89,113],"employs":[90],"pymupdf4llm":[91],"for":[92,128],"Markdown-preserving":[93],"PDF":[94],"extraction,":[95],"two-stage":[96],"document":[97],"chunking,":[98],"Maximal":[99],"Marginal":[100],"Relevance":[101],"retrieval,":[102],"topical":[104],"guardrail":[105],"that":[106,115],"filters":[107],"off-topic":[108],"queries,":[109],"specialized":[112],"prompt":[114],"prevents":[116],"exposure":[117],"internal":[119],"terminology.":[120],"A":[121],"dual-LLM":[122],"architecture":[123],"uses":[124],"separate":[125],"model":[126],"configurations":[127],"question":[129],"condensing":[130],"response":[132],"generation.":[133],"Deployed":[134],"production":[136],"Kubernetes":[138],"PostgreSQL":[140],"(pgvector),":[141],"it":[142],"provides":[143],"around-the-clock":[144],"depositor":[145],"assistance":[146],"citation-backed,":[148],"streaming":[149],"responses.":[150],"Availability":[151],"implementation:":[153],"Freely":[154],"available":[155],"at":[156],"https://rcsb-deposit-help.rcsb.org.":[157]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-04-29T00:00:00"}
