{"id":"https://openalex.org/W4412450099","doi":"https://doi.org/10.1007/s10822-025-00636-x","title":"Protein domain movement involved in binding of belinostat and HPOB as inhibitors of histone deacetylase 6 (HDAC6): a hybrid automated-interactive docking study","display_name":"Protein domain movement involved in binding of belinostat and HPOB as inhibitors of histone deacetylase 6 (HDAC6): a hybrid automated-interactive docking study","publication_year":2025,"publication_date":"2025-07-15","ids":{"openalex":"https://openalex.org/W4412450099","doi":"https://doi.org/10.1007/s10822-025-00636-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/40664741"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-025-00636-x","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-025-00636-x","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-025-00636-x.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10822-025-00636-x.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012058225","display_name":"Georgios Iakovou","orcid":null},"institutions":[{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]},{"id":"https://openalex.org/I2799472390","display_name":"Norfolk and Norwich University Hospital","ror":"https://ror.org/021zm6p18","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2799472390","https://openalex.org/I2800371493"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Georgios Iakovou","raw_affiliation_strings":["Digital Engineering, Aviva Plc, Norwich, Norfolk, NR1 3NS, UK","School of Computing Sciences, University East Anglia, Norwich, NR4 7TJ, UK"],"affiliations":[{"raw_affiliation_string":"Digital Engineering, Aviva Plc, Norwich, Norfolk, NR1 3NS, UK","institution_ids":["https://openalex.org/I2799472390"]},{"raw_affiliation_string":"School of Computing Sciences, University East Anglia, Norwich, NR4 7TJ, UK","institution_ids":["https://openalex.org/I1118541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012125834","display_name":"Leoni I. Palmer","orcid":"https://orcid.org/0000-0001-7894-0674"},"institutions":[{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"L. Palmer","raw_affiliation_strings":["School of Chemistry, Pharmacy, and Pharmacology, University East Anglia, Norwich, NR4 7TJ, UK"],"affiliations":[{"raw_affiliation_string":"School of Chemistry, Pharmacy, and Pharmacology, University East Anglia, Norwich, NR4 7TJ, UK","institution_ids":["https://openalex.org/I1118541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000189394","display_name":"A. Ganesan","orcid":"https://orcid.org/0000-0003-4862-7999"},"institutions":[{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"A. Ganesan","raw_affiliation_strings":["School of Chemistry, Pharmacy, and Pharmacology, University East Anglia, Norwich, NR4 7TJ, UK"],"affiliations":[{"raw_affiliation_string":"School of Chemistry, Pharmacy, and Pharmacology, University East Anglia, Norwich, NR4 7TJ, UK","institution_ids":["https://openalex.org/I1118541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035351286","display_name":"Akio Kitao","orcid":"https://orcid.org/0000-0002-5221-0806"},"institutions":[{"id":"https://openalex.org/I4210111488","display_name":"Life Science Institute","ror":"https://ror.org/01yeyd808","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210111488"]},{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akio Kitao","raw_affiliation_strings":["School of Life Science and Technology, Institute of Science Tokyo, Tokyo, 152-8550, Japan"],"affiliations":[{"raw_affiliation_string":"School of Life Science and Technology, Institute of Science Tokyo, Tokyo, 152-8550, Japan","institution_ids":["https://openalex.org/I4210111488","https://openalex.org/I114531698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085340045","display_name":"Stephen D. Laycock","orcid":"https://orcid.org/0000-0002-7724-1369"},"institutions":[{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stephen D. Laycock","raw_affiliation_strings":["School of Computing Sciences, University East Anglia, Norwich, NR4 7TJ, UK"],"affiliations":[{"raw_affiliation_string":"School of Computing Sciences, University East Anglia, Norwich, NR4 7TJ, UK","institution_ids":["https://openalex.org/I1118541"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023268539","display_name":"Steven Hayward","orcid":"https://orcid.org/0000-0001-6959-2604"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Steven Hayward","raw_affiliation_strings":["School of Computing Sciences, University East Anglia, Norwich, NR4 7TJ, UK. steven.hayward@uea.ac.uk"],"affiliations":[{"raw_affiliation_string":"School of Computing Sciences, University East Anglia, Norwich, NR4 7TJ, UK. steven.hayward@uea.ac.uk","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5012058225"],"corresponding_institution_ids":["https://openalex.org/I1118541","https://openalex.org/I2799472390"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":{"value":2890,"currency":"EUR","value_usd":3690},"fwci":0.8425,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.75003562,"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":"52","last_page":"52"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11736","display_name":"Histone Deacetylase Inhibitors Research","score":0.9998999834060669,"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/T11736","display_name":"Histone Deacetylase Inhibitors Research","score":0.9998999834060669,"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/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.9858999848365784,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12620","display_name":"Signaling Pathways in Disease","score":0.9810000061988831,"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/docking","display_name":"Docking (animal)","score":0.8146315813064575},{"id":"https://openalex.org/keywords/hdac6","display_name":"HDAC6","score":0.7881499528884888},{"id":"https://openalex.org/keywords/hydroxamic-acid","display_name":"Hydroxamic acid","score":0.7706888914108276},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6905368566513062},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.630551815032959},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5785202383995056},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5313620567321777},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.5146018266677856},{"id":"https://openalex.org/keywords/active-site","display_name":"Active site","score":0.46404120326042175},{"id":"https://openalex.org/keywords/binding-domain","display_name":"Binding domain","score":0.44303157925605774},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.4416205585002899},{"id":"https://openalex.org/keywords/histone-deacetylase","display_name":"Histone deacetylase","score":0.4348728060722351},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.36599159240722656},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.3274794816970825},{"id":"https://openalex.org/keywords/histone","display_name":"Histone","score":0.23795965313911438},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.14753177762031555},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1415254771709442},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12595173716545105}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8146315813064575},{"id":"https://openalex.org/C23681527","wikidata":"https://www.wikidata.org/wiki/Q18034953","display_name":"HDAC6","level":5,"score":0.7881499528884888},{"id":"https://openalex.org/C2776281265","wikidata":"https://www.wikidata.org/wiki/Q420327","display_name":"Hydroxamic acid","level":2,"score":0.7706888914108276},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6905368566513062},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.630551815032959},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5785202383995056},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5313620567321777},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.5146018266677856},{"id":"https://openalex.org/C41183919","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Active site","level":3,"score":0.46404120326042175},{"id":"https://openalex.org/C25166345","wikidata":"https://www.wikidata.org/wiki/Q4914012","display_name":"Binding domain","level":3,"score":0.44303157925605774},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4416205585002899},{"id":"https://openalex.org/C2778305200","wikidata":"https://www.wikidata.org/wiki/Q174378","display_name":"Histone deacetylase","level":4,"score":0.4348728060722351},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.36599159240722656},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.3274794816970825},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.23795965313911438},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.14753177762031555},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1415254771709442},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12595173716545105},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073864","descriptor_name":"Histone Deacetylase 6","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D000073864","descriptor_name":"Histone Deacetylase 6","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D000073864","descriptor_name":"Histone Deacetylase 6","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D000073864","descriptor_name":"Histone Deacetylase 6","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D000073864","descriptor_name":"Histone Deacetylase 6","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D000073864","descriptor_name":"Histone Deacetylase 6","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D000073864","descriptor_name":"Histone Deacetylase 6","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000073864","descriptor_name":"Histone Deacetylase 6","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000073864","descriptor_name":"Histone Deacetylase 6","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000073864","descriptor_name":"Histone Deacetylase 6","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000073864","descriptor_name":"Histone Deacetylase 6","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000073864","descriptor_name":"Histone Deacetylase 6","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":"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":"D006655","descriptor_name":"Histone Deacetylases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006655","descriptor_name":"Histone Deacetylases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006655","descriptor_name":"Histone Deacetylases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006655","descriptor_name":"Histone Deacetylases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006655","descriptor_name":"Histone Deacetylases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006655","descriptor_name":"Histone Deacetylases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006655","descriptor_name":"Histone Deacetylases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006655","descriptor_name":"Histone Deacetylases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006655","descriptor_name":"Histone Deacetylases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006655","descriptor_name":"Histone Deacetylases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006655","descriptor_name":"Histone Deacetylases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006655","descriptor_name":"Histone Deacetylases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"D006877","descriptor_name":"Hydroxamic Acids","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D006877","descriptor_name":"Hydroxamic Acids","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D006877","descriptor_name":"Hydroxamic Acids","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D006877","descriptor_name":"Hydroxamic Acids","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D006877","descriptor_name":"Hydroxamic Acids","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D006877","descriptor_name":"Hydroxamic Acids","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D006877","descriptor_name":"Hydroxamic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006877","descriptor_name":"Hydroxamic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006877","descriptor_name":"Hydroxamic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006877","descriptor_name":"Hydroxamic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006877","descriptor_name":"Hydroxamic Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006877","descriptor_name":"Hydroxamic Acids","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":"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":"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":"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":"D013449","descriptor_name":"Sulfonamides","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D013449","descriptor_name":"Sulfonamides","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D013449","descriptor_name":"Sulfonamides","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D013449","descriptor_name":"Sulfonamides","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D013449","descriptor_name":"Sulfonamides","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D013449","descriptor_name":"Sulfonamides","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D013449","descriptor_name":"Sulfonamides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013449","descriptor_name":"Sulfonamides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013449","descriptor_name":"Sulfonamides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013449","descriptor_name":"Sulfonamides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013449","descriptor_name":"Sulfonamides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013449","descriptor_name":"Sulfonamides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":"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":"D056572","descriptor_name":"Histone Deacetylase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D056572","descriptor_name":"Histone Deacetylase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D056572","descriptor_name":"Histone Deacetylase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D056572","descriptor_name":"Histone Deacetylase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D056572","descriptor_name":"Histone Deacetylase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D056572","descriptor_name":"Histone Deacetylase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D056572","descriptor_name":"Histone Deacetylase Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D056572","descriptor_name":"Histone Deacetylase Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D056572","descriptor_name":"Histone Deacetylase Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D056572","descriptor_name":"Histone Deacetylase Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D056572","descriptor_name":"Histone Deacetylase Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D056572","descriptor_name":"Histone Deacetylase Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1007/s10822-025-00636-x","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-025-00636-x","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-025-00636-x.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:40664741","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40664741","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},{"id":"pmh:oai:ueaeprints.uea.ac.uk:99946","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400384","display_name":"UEA Digital Repository (University of East Anglia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1118541","host_organization_name":"University of East Anglia","host_organization_lineage":["https://openalex.org/I1118541"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:pubmedcentral.nih.gov:12263812","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12263812","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12263812/pdf/10822_2025_Article_636.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Comput Aided Mol Des","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1007/s10822-025-00636-x","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-025-00636-x","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-025-00636-x.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.6600000262260437}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412450099.pdf","grobid_xml":"https://content.openalex.org/works/W4412450099.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1413301754","https://openalex.org/W1965270719","https://openalex.org/W1989920137","https://openalex.org/W1990265868","https://openalex.org/W1991161477","https://openalex.org/W2009129583","https://openalex.org/W2027486315","https://openalex.org/W2043329863","https://openalex.org/W2066690664","https://openalex.org/W2138934382","https://openalex.org/W2141970217","https://openalex.org/W2148383035","https://openalex.org/W2152630148","https://openalex.org/W2161870238","https://openalex.org/W2499955277","https://openalex.org/W2569372699","https://openalex.org/W2609167740","https://openalex.org/W2625712932","https://openalex.org/W2784827262","https://openalex.org/W2891791233","https://openalex.org/W2899876933","https://openalex.org/W2936106934","https://openalex.org/W2943039562","https://openalex.org/W2947642477","https://openalex.org/W2982032574","https://openalex.org/W2989052455","https://openalex.org/W3007469045","https://openalex.org/W3039236515","https://openalex.org/W3086801715","https://openalex.org/W3105639474","https://openalex.org/W3105643282","https://openalex.org/W3105968295","https://openalex.org/W3116310237","https://openalex.org/W3127412029","https://openalex.org/W3206226732","https://openalex.org/W4281660432","https://openalex.org/W4282917006","https://openalex.org/W4298198202","https://openalex.org/W4309364370","https://openalex.org/W4320732441","https://openalex.org/W4360599584","https://openalex.org/W4366351304","https://openalex.org/W4386392953","https://openalex.org/W4387332205","https://openalex.org/W4387440676","https://openalex.org/W4390562938","https://openalex.org/W4393201576","https://openalex.org/W4400485731","https://openalex.org/W4400571307","https://openalex.org/W4401105022","https://openalex.org/W4405583719","https://openalex.org/W4409240402","https://openalex.org/W4410141433"],"related_works":["https://openalex.org/W2081569115","https://openalex.org/W2045096823","https://openalex.org/W1965783758","https://openalex.org/W2037085251","https://openalex.org/W1967884598","https://openalex.org/W2134415371","https://openalex.org/W1988606508","https://openalex.org/W1978233546","https://openalex.org/W3046391818","https://openalex.org/W2889337982"],"abstract_inverted_index":{"DockIT":[0,36],"is":[1],"a":[2,25,31,73,85,102,136,165,171,213,254],"tool":[3],"for":[4,105,183,188,245],"interactive":[5],"molecular":[6,32,76],"docking":[7,23,100],"that":[8,88],"can":[9],"model":[10,61,104],"both":[11,122],"the":[12,19,22,40,51,57,66,69,82,90,95,106,108,113,116,119,141,146,151,155,198,206,220,223,226,230,235,238,243,246],"local":[13],"and":[14,56,92,101,145,161,185,225,237],"global":[15],"conformational":[16,63],"response":[17,64],"of":[18,24,43,68,94,118,180,205,215,222,240],"receptor":[20],"to":[21,49,65,115,258],"ligand":[26],"based":[27],"on":[28,79],"information":[29],"from":[30],"dynamics":[33,77],"simulation.":[34],"Using":[35,98],"we":[37,71],"have":[38],"investigated":[39],"binding":[41,67,96,126,167,204,212,252],"process":[42],"two":[44],"histone":[45],"deacetylase":[46],"(HDAC)":[47],"inhibitors":[48,70],"HDAC6:":[50],"nonselective":[52],"approved":[53],"drug":[54],"belinostat":[55,184],"preclinical":[58],"HPOB.":[59,189],"To":[60],"HDAC6's":[62],"performed":[72],"200-nanosecond":[74],"explicit-solvent":[75],"simulation":[78,83],"HDAC6.":[80],"Unexpectedly":[81],"revealed":[84],"domain":[86,109],"movement":[87,110],"affects":[89],"size":[91],"shape":[93],"pocket.":[97,231],"automated":[99,163],"rigid":[103],"inhibitors,":[107,123],"continuously":[111],"adapts":[112],"pocket":[114,156],"presence":[117],"inhibitor.":[120],"For":[121],"an":[124,158,201],"intermediate":[125],"site":[127],"was":[128,132],"found":[129],"where":[130],"it":[131],"partially":[133],"inserted,":[134],"with":[135,170,175,200,209],"hydrogen":[137,216],"bond":[138],"formed":[139],"between":[140,234],"inhibitor's":[142],"hydroxamic":[143,227,247],"acid":[144,228,248],"Tyr745":[147],"side":[148],"chain.":[149],"Pushing":[150],"inhibitor":[152],"deeper":[153],"into":[154],"over":[157],"energy":[159],"barrier":[160],"re-engaging":[162],"docking,":[164],"final":[166],"pose":[168,179],"resulted":[169],"root-mean":[172],"square":[173],"deviation":[174],"its":[176],"respective":[177],"crystallographic":[178],"1.0":[181],"\u00c5":[182,187],"1.4":[186],"We":[190],"believe":[191],"our":[192],"results":[193],"mimic":[194],"substrate":[195],"recognition":[196],"by":[197],"enzyme,":[199],"initial":[202],"partial":[203],"acetyllysine":[207],"residue":[208],"Tyr745.":[210],"During":[211],"relay":[214],"bonds":[217],"occurs":[218],"coordinating":[219],"orientation":[221,256],"cap":[224,236],"inside":[229],"The":[232],"interaction":[233],"surface":[239],"HDAC6":[241],"explains":[242],"reason":[244],"warhead":[249],"in":[250,253],"HPOB":[251],"flipped":[255],"compared":[257],"belinostat.":[259]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}