{"doi":"10.1107/s2052252518010552","title":"Homology-based loop modeling yields more complete crystallographic protein structures","abstract":"<jats:p>\n                    Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and `graft' these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in the\n                    <jats:italic>PDB-REDO</jats:italic>\n                    pipeline has enabled the building of 24 962 missing loops in the PDB. The models and the automated procedures are publicly available through the PDB-REDO databank and webserver. More complete protein structure models enable a higher quality public archive but also a better understanding of protein function, better comparison between homologous structures and more complete data mining in structural bioinformatics projects.\n                  </jats:p>","journal":"IUCrJ","year":2018,"id":15391,"datarank":1.3226562460311833,"base_score":3.5553480614894135,"endowment":3.5553480614894135,"self_citation_contribution":0.5333022092234121,"citation_network_contribution":0.7893540368077713,"self_endowment_contribution":0.5333022092234121,"citer_contribution":0.7893540368077713,"corpus_percentile":null,"corpus_rank":null,"citation_count":34,"citer_count":22,"citers_with_citation_signal":20,"citers_with_endowment":20,"datacite_reuse_total":1,"is_dataset":false,"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":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":117598,"name":"Krista Joosten","orcid":null,"position":1,"is_corresponding":false},{"id":117599,"name":"Maarten L. Hekkelman","orcid":"0000-0002-9081-4707","position":2,"is_corresponding":false},{"id":117600,"name":"Robbie P. Joosten","orcid":"0000-0002-2323-2686","position":3,"is_corresponding":false},{"id":117601,"name":"Anastassis Perrakis","orcid":"0000-0002-1151-6227","position":4,"is_corresponding":false},{"id":117597,"name":"Bart van Beusekom","orcid":"0000-0002-2183-2901","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":3.5553480614894135,"endowment":3.5553480614894135,"datacite_reuse_total":1,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"30224962","pmcid":"PMC6126648","openalex_id":"https://openalex.org/W2803843415","authors":[],"funders":[{"funder_name":"Netherlands Organization for Scientific Research","grant_id":"723.013.003","title":"Optimised protein structures through transfer of evolutionary conserved features and chemical knowledge"},{"funder_name":"European Comission Horizon 2020 programme","grant_id":"675858","title":"World-wide E-infrastructure for structural biology"},{"funder_name":"European Comission Horizon 2020 programme","grant_id":"653706","title":"Infrastructure for NMR, EM and X-rays for translational research"}],"total_grants":3,"fwci":1.7813,"citation_percentile":0.8482208,"influential_citations":0,"citation_trend":[{"year":2018,"count":1},{"year":2019,"count":5},{"year":2020,"count":8},{"year":2021,"count":4},{"year":2022,"count":4},{"year":2023,"count":5},{"year":2024,"count":5},{"year":2025,"count":2}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://journals.iucr.org/m/issues/2018/05/00/jt5027/jt5027.pdf","host_type":"journal"},{"url":"https://journals.iucr.org/m/issues/2018/05/00/jt5027/jt5027.pdf","host_type":"GOLD"},{"url":"https://journals.iucr.org/m/issues/2018/05/00/jt5027/jt5027.pdf","host_type":"publisher"},{"url":"http://journals.iucr.org/m/issues/2018/05/00/jt5027/jt5027.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1107/s2052252518010552","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/30224962","host_type":"repository"},{"url":"https://doaj.org/article/0ee3c8f9483c4b9c83b6307d26619448","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6126648","host_type":"repository"},{"url":"http://doi.org/10.1107/S2052252518010552","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC6126648","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC6126648?pdf=render","host_type":"Europe_PMC"},{"url":"https://doi.org/10.1101/329219","host_type":""},{"url":"https://www.biorxiv.org/content/biorxiv/early/2018/05/23/329219.full.pdf","host_type":""},{"url":"http://dx.doi.org/10.1107/S2052252518010552","host_type":""},{"url":"https://dx.doi.org/10.1107/s2052252518010552","host_type":""},{"url":"https://dx.doi.org/10.1101/329219","host_type":""},{"url":"http://dx.doi.org/10.1107/s2052252518010552","host_type":""},{"url":"http://dx.doi.org/10.1101/329219","host_type":""}],"fields_of_study":["Enzyme Structure and Function","Protein Structure and Dynamics","Microbial Metabolic Engineering and Bioproduction","Computer Science","Medicine","Biology","Materials Science","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":[],"keywords":["Protein Data Bank (RCSB PDB)","Protein Data Bank","Computer science","Protein structure database","Loop modeling","Pipeline (software)","Homology modeling","Data mining","Protein superfamily","Structural bioinformatics","Protein structure","Flexibility (engineering)","Model building","Computational biology","Software","Bioinformatics","Crystallography","Protein structure prediction","Biology","Chemistry","Programming language","Genetics","Mathematics","Physics","Model Completion","Pdb-redo","Loop Building","Structural Re-building","QD901-999","Research Papers"],"sdg_mappings":[],"linked_datasets":[{"doi":"10.25504/fairsharing.d02054","title":"FAIRsharing record for: PDB-REDO","publisher":"FAIRsharing","resource_type":"Dataset"}],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"pdb"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-01T17:31:27.946466Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}