{"doi":"10.1021/ci2005687","title":"ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of PDB Structures","abstract":null,"journal":"Journal of Chemical Information and Modeling","year":2012,"id":16312,"datarank":2.1873546435646896,"base_score":4.02535169073515,"endowment":4.02535169073515,"self_citation_contribution":0.6038027536102726,"citation_network_contribution":1.583551889954417,"self_endowment_contribution":0.6038027536102726,"citer_contribution":1.583551889954417,"corpus_percentile":90.2993734045022,"corpus_rank":1255,"citation_count":55,"citer_count":37,"citers_with_citation_signal":32,"citers_with_endowment":32,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":47.9167,"fair_percentile":43.4878587196468,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":120858,"name":"Tomo Česnik","orcid":null,"position":1,"is_corresponding":false},{"id":120859,"name":"Joanna Trykowska Konc","orcid":null,"position":2,"is_corresponding":false},{"id":120860,"name":"Matej Penca","orcid":null,"position":3,"is_corresponding":false},{"id":120861,"name":"Dušanka Janežič","orcid":null,"position":4,"is_corresponding":false},{"id":120857,"name":"Janez Konc","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":4.02535169073515,"endowment":4.02535169073515,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"22268964","pmcid":"PMC3287116","openalex_id":"https://openalex.org/W1973462822","authors":[],"funders":[],"total_grants":0,"fwci":2.7177,"citation_percentile":0.90661161,"influential_citations":3,"citation_trend":[{"year":2012,"count":5},{"year":2013,"count":5},{"year":2014,"count":3},{"year":2015,"count":5},{"year":2016,"count":7},{"year":2017,"count":7},{"year":2018,"count":3},{"year":2019,"count":4},{"year":2020,"count":3},{"year":2021,"count":5},{"year":2022,"count":2},{"year":2023,"count":3},{"year":2025,"count":1},{"year":2026,"count":2}],"oa_status":"hybrid","license":"other-oa","oa_locations":[{"url":"https://doi.org/10.1021/ci2005687","host_type":"journal"},{"url":"https://doi.org/10.1021/ci2005687","host_type":"HYBRID"},{"url":"https://doi.org/10.1021/ci2005687","host_type":"publisher"},{"url":"https://pubs.acs.org/doi/pdf/10.1021/ci2005687","host_type":"publisher"},{"url":"https://pubmed.ncbi.nlm.nih.gov/22268964","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3287116","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC3287116","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC3287116?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Enzyme Structure and Function","Protein Structure and Dynamics","Glycosylation and Glycoproteins Research","Medicine","Computer Science","Biology","Algorithms","Binding Sites","Databases, Protein","Internet","Protein Conformation","Proteins","Structural Homology, Protein"],"mesh_terms":["Algorithms","Binding Sites","Protein Conformation","Proteins","Internet","Databases, Protein","Structural Homology, Protein"],"keywords":["Protein Data Bank (RCSB PDB)","Protein Data Bank","Protein structure database","Database","Computer science","Structural similarity","Protein structure","Structural bioinformatics","Pairwise comparison","Structural Classification of Proteins database","Structural alignment","Interface (matter)","Identification (biology)","Similarity (geometry)","Data mining","Information retrieval","Computational biology","Sequence database","Sequence alignment","Biology","Peptide sequence","Genetics","Artificial intelligence"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Partnerships for the goals"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"pfam"},{"name":"pdb"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-01T21:23:06.512324Z","pmid":"22268964","pmcid":"PMC3287116","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"hybrid","license":"other-oa","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":40.0,"fair_a":72.5,"fair_i":37.5,"fair_r":41.6667,"fair_zscore":-0.207,"fair_rationale":{"fair_score":47.92,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":40.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.0,"signal":null,"rationale":"The paper provides no description of machine-readable metadata (e.g., schema.org annotations, RDF, or structured metadata) to enhance findability beyond a plain web interface."}]},"A":{"name":"Accessible","score":72.5,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":0.5,"signal":"files/OA location present but not flagged OA","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"8 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"Access is clearly described via a search text box, a widget, and a RESTful Web Service interface with HTTP commands and formats (JSON, XML, text/plain), but no explicit authentication or persistent identifier (other than PDB IDs) is mandated."}]},"I":{"name":"Interoperable","score":37.5,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"The database uses standard PDB identifiers and Pfam classifications, and the RESTful service supports JSON, XML, and text/plain formats, but no formal community-wide standard for metadata or vocabularies is explicitly adopted beyond these."}]},"R":{"name":"Reusable","score":41.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.667,"signal":null,"rationale":"The paper describes weekly updates, free online availability, and an open access license (ACS AuthorChoice), but no explicit data availability statement, license for reuse, or repository link for data/code is provided, and reproducibility of the full database generation is not detailed enough for independent replication."}]}},"suggestions":["Include machine-readable metadata (e.g., JSON-LD with schema.org) on the database home page and in data outputs.","Provide a persistent identifier (e.g., DOI) for the database itself and for each major version or release.","Formally define a license (e.g., Creative Commons Attribution) for reuse of the database content and alignments.","Publish the raw alignment data or a subset in a recognized public repository (e.g., Zenodo or Figshare) with a separate data availability statement.","Document the full workflow, parameters, and software versions in a way that allows full reproducibility of the ProBiS-Database construction."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:42:52.267348Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}