{"doi":"10.1093/nar/gkl412","title":"Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility","abstract":null,"journal":"Nucleic Acids Research","year":2006,"id":595223,"datarank":0.7854662944244925,"base_score":5.236441962829949,"endowment":5.236441962829949,"self_citation_contribution":0.7854662944244925,"citation_network_contribution":0.0,"self_endowment_contribution":0.7854662944244925,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":187,"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":1524103,"name":"M. van Dijk","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility","abstract":"Intrinsic flexibility of DNA has hampered the development of efficient protein-DNA docking methods. In this study we extend HADDOCK (High Ambiguity Driven DOCKing) [C. Dominguez, R. Boelens and A. M. J. J. Bonvin (2003) J. Am. Chem. Soc. 125, 1731-1737] to explicitly deal with DNA flexibility. HADDOCK uses non-structural experimental data to drive the docking during a rigid-body energy minimization, and semi-flexible and water refinement stages. The latter allow for flexibility of all DNA nucleotides and the residues of the protein at the predicted interface. We evaluated our approach on the monomeric repressor-DNA complexes formed by bacteriophage 434 Cro, the Escherichia coli Lac headpiece and bacteriophage P22 Arc. Starting from unbound proteins and canonical B-DNA we correctly predict the correct spatial disposition of the complexes and the specific conformation of the DNA in the published complexes. This information is subsequently used to generate a library of pre-bent and twisted DNA structures that served as input for a second docking round. The resulting top ranking solutions exhibit high similarity to the published complexes in terms of root mean square deviations, intermolecular contacts and DNA conformation. Our two-stage docking method is thus able to successfully predict protein-DNA complexes from unbound constituents using non-structural experimental data to drive the docking.","is_dataset_classified":null,"base_score":5.236441962829949,"endowment":5.236441962829949,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"16820531","pmcid":"PMC1500871","openalex_id":"https://openalex.org/W2099857980","authors":[],"funders":[{"funder_name":"Dutch Research Council (NWO)","grant_id":"700.52.303","title":"Structural investigations of gene regulation by NMR spectroscopy."}],"total_grants":1,"fwci":4.1931,"citation_percentile":0.94868405,"influential_citations":0,"citation_trend":[{"year":2012,"count":16},{"year":2013,"count":12},{"year":2014,"count":11},{"year":2015,"count":15},{"year":2016,"count":10},{"year":2017,"count":5},{"year":2018,"count":10},{"year":2019,"count":7},{"year":2020,"count":3},{"year":2021,"count":5},{"year":2022,"count":9},{"year":2023,"count":4},{"year":2024,"count":3},{"year":2025,"count":6},{"year":2026,"count":6}],"oa_status":"gold","license":"cc-by-nc","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/34/11/3317/3672999/gkl412.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/34/11/3317/3672999/gkl412.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/nar/article-pdf/34/11/3317/3672999/gkl412.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkl412","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/16820531","host_type":"repository"},{"url":"https://research.vu.nl/en/publications/b9394b28-7b4d-4b69-993e-dba8ddcd376b","host_type":"repository"},{"url":"https://dspace.library.uu.nl/handle/1874/20111","host_type":"repository"},{"url":"http://europepmc.org/pmc/articles/PMC1500871","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1500871","host_type":"repository"},{"url":"https://hdl.handle.net/1871.1/b9394b28-7b4d-4b69-993e-dba8ddcd376b","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC1500871","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC1500871?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1093/nar/gkl412","host_type":""},{"url":"https://research-portal.uu.nl/en/publications/3f037c44-ee6c-40b2-98d8-cae36bfa62c7","host_type":""},{"url":"https://dx.doi.org/10.1093/nar/gkl412","host_type":""}],"fields_of_study":["RNA and protein synthesis mechanisms","Bacteriophages and microbial interactions","DNA and Nucleic Acid Chemistry","0301 basic medicine","0303 health sciences","03 medical and health sciences","Computational Biology","DNA","DNA-Binding Proteins","Escherichia coli Proteins","Models, Molecular","Motion","Repressor Proteins","Software","Viral Proteins","Viral Regulatory and Accessory Proteins"],"mesh_terms":["DNA","DNA-Binding Proteins","Models, Molecular","Motion","Repressor Proteins","Software","Viral Proteins","Computational Biology","Escherichia coli Proteins","Viral Regulatory and Accessory Proteins"],"keywords":["Docking (animal)","DNA","Biology","Searching the conformational space for docking","Protein–ligand docking","Molecular dynamics","Computational biology","Crystallography","Protein structure","Biophysics","Biochemistry","Virtual screening","Computational chemistry","Chemistry","Drug discovery","Models, Molecular","Escherichia coli Proteins","Article","DNA-Binding Proteins","Repressor Proteins","Motion","Viral Proteins","Viral Regulatory and Accessory Proteins","Software"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Clean water and sanitation"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"pdb"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-27T16:54:26.811346Z","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":[]}