{"id":"https://openalex.org/W4411771983","doi":"https://doi.org/10.1007/s10822-025-00613-4","title":"Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones","display_name":"Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones","publication_year":2025,"publication_date":"2025-06-29","ids":{"openalex":"https://openalex.org/W4411771983","doi":"https://doi.org/10.1007/s10822-025-00613-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/40581880"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-025-00613-4","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-025-00613-4","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/A5021301796","display_name":"Vladimir Porokhin","orcid":"https://orcid.org/0000-0003-3291-642X"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Vladimir Porokhin","raw_affiliation_strings":["Department of Computer Science, Tufts University, Medford, MA, 02155, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Tufts University, Medford, MA, 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081565182","display_name":"Anne M. Brown","orcid":"https://orcid.org/0000-0001-6951-8228"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anne M. Brown","raw_affiliation_strings":["Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24060, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Virginia Tech, Blacksburg, VA, 24060, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048817284","display_name":"Soha Hassoun","orcid":"https://orcid.org/0000-0001-9477-2199"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Soha Hassoun","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Tufts University, Medford, MA, 02155, USA. soha.hassoun@tufts.edu","Department of Computer Science, Tufts University, Medford, MA, 02155, USA. soha.hassoun@tufts.edu"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Tufts University, Medford, MA, 02155, USA. soha.hassoun@tufts.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, Tufts University, Medford, MA, 02155, USA. soha.hassoun@tufts.edu","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5021301796"],"corresponding_institution_ids":["https://openalex.org/I121934306"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":0.8734,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.75049363,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"39","issue":"1","first_page":"39","last_page":"39"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12763","display_name":"ATP Synthase and ATPases Research","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12763","display_name":"ATP Synthase and ATPases Research","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10303","display_name":"Photosynthetic Processes and Mechanisms","score":0.9900000095367432,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9879000186920166,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.7113310694694519},{"id":"https://openalex.org/keywords/oxidoreductase","display_name":"Oxidoreductase","score":0.6607786417007446},{"id":"https://openalex.org/keywords/quinone","display_name":"Quinone","score":0.6601755619049072},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.6290718913078308},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.39189469814300537},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3499413728713989},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.33022546768188477},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.27818402647972107},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.07691359519958496}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.7113310694694519},{"id":"https://openalex.org/C2779268744","wikidata":"https://www.wikidata.org/wiki/Q407479","display_name":"Oxidoreductase","level":3,"score":0.6607786417007446},{"id":"https://openalex.org/C2780643102","wikidata":"https://www.wikidata.org/wiki/Q412382","display_name":"Quinone","level":2,"score":0.6601755619049072},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6290718913078308},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.39189469814300537},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3499413728713989},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.33022546768188477},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.27818402647972107},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.07691359519958496}],"mesh":[{"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":"D004579","descriptor_name":"Electron Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004579","descriptor_name":"Electron Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004579","descriptor_name":"Electron Transport","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":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009245","descriptor_name":"NADH Dehydrogenase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009245","descriptor_name":"NADH Dehydrogenase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009245","descriptor_name":"NADH Dehydrogenase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009245","descriptor_name":"NADH Dehydrogenase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D009245","descriptor_name":"NADH Dehydrogenase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D009245","descriptor_name":"NADH Dehydrogenase","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":"D011808","descriptor_name":"Quinone Reductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011808","descriptor_name":"Quinone Reductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011808","descriptor_name":"Quinone Reductases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011808","descriptor_name":"Quinone Reductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011808","descriptor_name":"Quinone Reductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011808","descriptor_name":"Quinone Reductases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011809","descriptor_name":"Quinones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011809","descriptor_name":"Quinones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011809","descriptor_name":"Quinones","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011809","descriptor_name":"Quinones","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011809","descriptor_name":"Quinones","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011809","descriptor_name":"Quinones","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-025-00613-4","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-025-00613-4","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:40581880","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40581880","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":[{"id":"https://openalex.org/G4657142875","display_name":null,"funder_award_id":"W911NF2210239","funder_id":"https://openalex.org/F4320338281","funder_display_name":"Army Research Office"}],"funders":[{"id":"https://openalex.org/F4320338281","display_name":"Army Research Office","ror":"https://ror.org/05epdh915"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1921909110","https://openalex.org/W1956858148","https://openalex.org/W1992192767","https://openalex.org/W2002874263","https://openalex.org/W2010356367","https://openalex.org/W2022806195","https://openalex.org/W2031168104","https://openalex.org/W2049631297","https://openalex.org/W2084600753","https://openalex.org/W2106154817","https://openalex.org/W2106383417","https://openalex.org/W2115167726","https://openalex.org/W2115948190","https://openalex.org/W2129153475","https://openalex.org/W2129434797","https://openalex.org/W2134967712","https://openalex.org/W2138073891","https://openalex.org/W2142678478","https://openalex.org/W2171419407","https://openalex.org/W2336040088","https://openalex.org/W2345374791","https://openalex.org/W2571059898","https://openalex.org/W2588635793","https://openalex.org/W2751260413","https://openalex.org/W2766865386","https://openalex.org/W2804822363","https://openalex.org/W2892082086","https://openalex.org/W2912212024","https://openalex.org/W2956569764","https://openalex.org/W2970628659","https://openalex.org/W2987335406","https://openalex.org/W3000763633","https://openalex.org/W3014154196","https://openalex.org/W3093687066","https://openalex.org/W3112376646","https://openalex.org/W3144239152","https://openalex.org/W3177828909","https://openalex.org/W3185760697","https://openalex.org/W3186179742","https://openalex.org/W3205470891","https://openalex.org/W3209056694","https://openalex.org/W3211795435","https://openalex.org/W4234714728","https://openalex.org/W4307468223","https://openalex.org/W4318071656","https://openalex.org/W4366819307","https://openalex.org/W4379619640","https://openalex.org/W4386100532","https://openalex.org/W4387710948","https://openalex.org/W4392858757","https://openalex.org/W4393387663","https://openalex.org/W4396721167","https://openalex.org/W4403324307","https://openalex.org/W4404208829","https://openalex.org/W4404565424","https://openalex.org/W4405184031","https://openalex.org/W4406452735"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2141133578","https://openalex.org/W2100568099","https://openalex.org/W2071974159","https://openalex.org/W1499056254","https://openalex.org/W2953219586","https://openalex.org/W3082145469","https://openalex.org/W4244178463","https://openalex.org/W2053802655","https://openalex.org/W4392354784"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
