{"id":"https://openalex.org/W4415847061","doi":"https://doi.org/10.1007/s10822-025-00692-3","title":"Elucidating ligand recognition of reductive dehalogenases: the role of hydrophobic active site in organohalogen binding","display_name":"Elucidating ligand recognition of reductive dehalogenases: the role of hydrophobic active site in organohalogen binding","publication_year":2025,"publication_date":"2025-11-04","ids":{"openalex":"https://openalex.org/W4415847061","doi":"https://doi.org/10.1007/s10822-025-00692-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/41186804"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-025-00692-3","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-025-00692-3","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015283451","display_name":"Yi Ren","orcid":"https://orcid.org/0000-0002-0176-493X"},"institutions":[{"id":"https://openalex.org/I4210123971","display_name":"Kensington Health","ror":"https://ror.org/02qcscp23","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210123971"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU","CA"],"is_corresponding":true,"raw_author_name":"Yi Ren","raw_affiliation_strings":["Water Research Centre, UNSW Sydney, Kensington, Australia"],"affiliations":[{"raw_affiliation_string":"Water Research Centre, UNSW Sydney, Kensington, Australia","institution_ids":["https://openalex.org/I4210123971","https://openalex.org/I31746571"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041678529","display_name":"Michael Manefield","orcid":"https://orcid.org/0000-0002-1880-0888"},"institutions":[{"id":"https://openalex.org/I4210123971","display_name":"Kensington Health","ror":"https://ror.org/02qcscp23","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210123971"]},{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU","CA"],"is_corresponding":false,"raw_author_name":"Mike Manefield","raw_affiliation_strings":["Water Research Centre, UNSW Sydney, Kensington, Australia. manefield@unsw.edu.au","Water Research Centre, UNSW Sydney, Kensington, Australia"],"affiliations":[{"raw_affiliation_string":"Water Research Centre, UNSW Sydney, Kensington, Australia. manefield@unsw.edu.au","institution_ids":[]},{"raw_affiliation_string":"Water Research Centre, UNSW Sydney, Kensington, Australia","institution_ids":["https://openalex.org/I4210123971","https://openalex.org/I31746571"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5015283451"],"corresponding_institution_ids":["https://openalex.org/I31746571","https://openalex.org/I4210123971"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.27217278,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"39","issue":"2","first_page":"115","last_page":"115"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10324","display_name":"Microbial bioremediation and biosurfactants","score":0.8210999965667725,"subfield":{"id":"https://openalex.org/subfields/2310","display_name":"Pollution"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10324","display_name":"Microbial bioremediation and biosurfactants","score":0.8210999965667725,"subfield":{"id":"https://openalex.org/subfields/2310","display_name":"Pollution"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12078","display_name":"Environmental remediation with nanomaterials","score":0.06650000065565109,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11180","display_name":"Pesticide and Herbicide Environmental Studies","score":0.03370000049471855,"subfield":{"id":"https://openalex.org/subfields/2310","display_name":"Pollution"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/solvation","display_name":"Solvation","score":0.8632000088691711},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.6201000213623047},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5532000064849854},{"id":"https://openalex.org/keywords/reactivity","display_name":"Reactivity (psychology)","score":0.5199000239372253},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.4708999991416931},{"id":"https://openalex.org/keywords/active-site","display_name":"Active site","score":0.4659000039100647},{"id":"https://openalex.org/keywords/van-der-waals-force","display_name":"van der Waals force","score":0.46470001339912415},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.430400013923645}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.9052000045776367},{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.8632000088691711},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6201000213623047},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5532000064849854},{"id":"https://openalex.org/C2776910235","wikidata":"https://www.wikidata.org/wiki/Q18574","display_name":"Reactivity (psychology)","level":3,"score":0.5199000239372253},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.4708999991416931},{"id":"https://openalex.org/C41183919","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Active site","level":3,"score":0.4659000039100647},{"id":"https://openalex.org/C126061179","wikidata":"https://www.wikidata.org/wiki/Q189627","display_name":"van der Waals force","level":3,"score":0.46470001339912415},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.4388999938964844},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.430400013923645},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4077000021934509},{"id":"https://openalex.org/C64147673","wikidata":"https://www.wikidata.org/wiki/Q6007318","display_name":"Implicit solvation","level":4,"score":0.397599995136261},{"id":"https://openalex.org/C29705727","wikidata":"https://www.wikidata.org/wiki/Q294562","display_name":"Polar","level":2,"score":0.3578000068664551},{"id":"https://openalex.org/C22499117","wikidata":"https://www.wikidata.org/wiki/Q2253702","display_name":"Interaction energy","level":3,"score":0.3553999960422516},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.3441999852657318},{"id":"https://openalex.org/C90260826","wikidata":"https://www.wikidata.org/wiki/Q899157","display_name":"Hydrophobic effect","level":2,"score":0.34360000491142273},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.33809998631477356},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.310699999332428},{"id":"https://openalex.org/C20803032","wikidata":"https://www.wikidata.org/wiki/Q207900","display_name":"QM/MM","level":3,"score":0.30480000376701355},{"id":"https://openalex.org/C2777485300","wikidata":"https://www.wikidata.org/wiki/Q5252213","display_name":"Dehalogenase","level":3,"score":0.2838999927043915},{"id":"https://openalex.org/C179303850","wikidata":"https://www.wikidata.org/wiki/Q4300362","display_name":"Molecular recognition","level":3,"score":0.2800000011920929},{"id":"https://openalex.org/C175634916","wikidata":"https://www.wikidata.org/wiki/Q17075777","display_name":"Potential of mean force","level":3,"score":0.2533000111579895}],"mesh":[{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010088","descriptor_name":"Oxidoreductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054879","descriptor_name":"Halogenation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054879","descriptor_name":"Halogenation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054879","descriptor_name":"Halogenation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-025-00692-3","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-025-00692-3","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:41186804","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41186804","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of computer-aided molecular design","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":84,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1969046853","https://openalex.org/W1971275758","https://openalex.org/W1975580333","https://openalex.org/W1976499671","https://openalex.org/W1978330227","https://openalex.org/W1982595063","https://openalex.org/W1997639796","https://openalex.org/W2004224330","https://openalex.org/W2005386550","https://openalex.org/W2011601475","https://openalex.org/W2013759011","https://openalex.org/W2017713125","https://openalex.org/W2021520922","https://openalex.org/W2021534482","https://openalex.org/W2022890083","https://openalex.org/W2030841140","https://openalex.org/W2030971064","https://openalex.org/W2038968184","https://openalex.org/W2041790717","https://openalex.org/W2044172327","https://openalex.org/W2047730466","https://openalex.org/W2049996223","https://openalex.org/W2052822239","https://openalex.org/W2056097827","https://openalex.org/W2057477511","https://openalex.org/W2064526878","https://openalex.org/W2073023478","https://openalex.org/W2075544881","https://openalex.org/W2079591552","https://openalex.org/W2081693079","https://openalex.org/W2088222298","https://openalex.org/W2092157292","https://openalex.org/W2106140689","https://openalex.org/W2117620409","https://openalex.org/W2128572087","https://openalex.org/W2129219923","https://openalex.org/W2132525235","https://openalex.org/W2139842115","https://openalex.org/W2142878254","https://openalex.org/W2143981217","https://openalex.org/W2147993766","https://openalex.org/W2148284063","https://openalex.org/W2153794904","https://openalex.org/W2165779834","https://openalex.org/W2166796013","https://openalex.org/W2170711116","https://openalex.org/W2233917167","https://openalex.org/W2285379289","https://openalex.org/W2333083696","https://openalex.org/W2340832150","https://openalex.org/W2404280981","https://openalex.org/W2491390835","https://openalex.org/W2495928889","https://openalex.org/W2606940716","https://openalex.org/W2692584004","https://openalex.org/W2751468153","https://openalex.org/W2752899739","https://openalex.org/W2766437757","https://openalex.org/W2767998122","https://openalex.org/W2783351753","https://openalex.org/W2795828290","https://openalex.org/W2904555348","https://openalex.org/W2996015651","https://openalex.org/W3005365002","https://openalex.org/W3012242125","https://openalex.org/W3017580640","https://openalex.org/W3094856358","https://openalex.org/W3135342255","https://openalex.org/W3169042931","https://openalex.org/W3205838659","https://openalex.org/W3211761789","https://openalex.org/W4206049800","https://openalex.org/W4292084531","https://openalex.org/W4308072855","https://openalex.org/W4319984891","https://openalex.org/W4328100119","https://openalex.org/W4381618728","https://openalex.org/W4384831965","https://openalex.org/W4399012917","https://openalex.org/W4401153365","https://openalex.org/W4402596009","https://openalex.org/W4404950115","https://openalex.org/W4407713934"],"related_works":[],"abstract_inverted_index":null,"counts_by_year":[],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-11-04T00:00:00"}
