{"doi":"10.1007/978-1-4939-3572-7_5","title":"Classification and Exploration of 3D Protein Domain Interactions Using Kbdock","abstract":null,"journal":"Methods in Molecular Biology","year":2016,"id":637175,"datarank":0.31191623125197543,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"self_citation_contribution":0.31191623125197543,"citation_network_contribution":0.0,"self_endowment_contribution":0.31191623125197543,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"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":29870,"name":"Marie-Dominique Devignes","orcid":null,"position":1,"is_corresponding":false},{"id":29871,"name":"Malika Smaïl-Tabbone","orcid":null,"position":2,"is_corresponding":false},{"id":122155,"name":"David W. Ritchie","orcid":null,"position":3,"is_corresponding":false},{"id":231118,"name":"Anisah W. Ghoorah","orcid":"0000-0001-8273-6000","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Classification and Exploration of 3D Protein Domain Interactions Using Kbdock","abstract":"Comparing and classifying protein domain interactions according to their three-dimensional (3D) structures can help to understand protein structure-function and evolutionary relationships. Additionally, structural knowledge of existing domain-domain interactions can provide a useful way to find structural templates with which to model the 3D structures of unsolved protein complexes. Here we present a straightforward guide to using the \"Kbdock\" protein domain structure database and its associated web site for exploring and comparing protein domain-domain interactions (DDIs) and domain-peptide interactions (DPIs) at the Pfam domain family level. We also briefly explain how the Kbdock web site works, and we provide some notes and suggestions which should help to avoid some common pitfalls when working with 3D protein domain structures.","is_dataset_classified":null,"base_score":2.0794415416798357,"endowment":2.0794415416798357,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"27115629","pmcid":null,"openalex_id":"https://openalex.org/W2499073244","authors":[],"funders":[],"total_grants":0,"fwci":2.5763,"citation_percentile":0.89279095,"influential_citations":0,"citation_trend":[{"year":2018,"count":2},{"year":2019,"count":3},{"year":2021,"count":1},{"year":2022,"count":1}],"oa_status":"closed","license":"http://www.springer.com/tdm","oa_locations":[{"url":"http://link.springer.com/content/pdf/10.1007/978-1-4939-3572-7_5","host_type":"publisher"},{"url":"https://doi.org/10.1007/978-1-4939-3572-7_5","host_type":"book series"},{"url":"https://pubmed.ncbi.nlm.nih.gov/27115629","host_type":"repository"},{"url":"https://inria.hal.science/hal-01317448","host_type":"repository"}],"fields_of_study":["Protein Structure and Dynamics","Enzyme Structure and Function","Bioinformatics and Genomic Networks","Databases, Protein","Internet","Models, Molecular","Molecular Docking Simulation","Protein Binding","Protein Domains","Protein Interaction Domains and Motifs","Protein Interaction Maps","Protein Structure, Secondary","Protein Structure, Tertiary","Proteins"],"mesh_terms":["Protein Domains","Models, Molecular","Protein Binding","Proteins","Protein Structure, Secondary","Protein Structure, Tertiary","Internet","Databases, Protein","Protein Interaction Domains and Motifs","Protein Interaction Maps","Molecular Docking Simulation"],"keywords":["Domain (mathematical analysis)","Protein domain","Computer science","Domain model","Function (biology)","Template","Protein structure","Computational biology","Protein function","Protein–protein interaction","Protein structure prediction","Data mining","Artificial intelligence","Domain knowledge","Biology","Evolutionary biology","Genetics","Mathematics","Biochemistry","Protein domains","Structural homology","Structural Biology","Domain Family Binding Sites","Domain Family Interactions","Domain–domain Interactions","Domain–peptide Interactions","Protein Domain Family"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-06T18:27:42.718728Z","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":[]}