{"id":"https://openalex.org/W7223180932","doi":"https://doi.org/10.26434/chemrxiv.15010882/v1","title":"Water-Model Dependence of Absolute Binding Free Energies across the Bromodomain Family","display_name":"Water-Model Dependence of Absolute Binding Free Energies across the Bromodomain Family","publication_year":2026,"publication_date":"2026-10-22","ids":{"openalex":"https://openalex.org/W7223180932","doi":"https://doi.org/10.26434/chemrxiv.15010882/v1"},"language":"en","primary_location":{"id":"doi:10.26434/chemrxiv.15010882/v1","doi":"https://doi.org/10.26434/chemrxiv.15010882/v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.15010882/v1","pdf_url":"https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15010882/v1","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":null,"raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15010882/v1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5159246933","display_name":"Ege Altun","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I41641357","display_name":"Ege University","ror":"https://ror.org/02eaafc18","country_code":"TR","type":"education","lineage":["https://openalex.org/I41641357"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ege Altun","raw_affiliation_strings":["Ege University","Faculty of Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ege University","institution_ids":["https://openalex.org/I41641357"]},{"raw_affiliation_string":"Faculty of Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038976999","display_name":"\u0130pek Sar\u0131bal","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I41641357","display_name":"Ege University","ror":"https://ror.org/02eaafc18","country_code":"TR","type":"education","lineage":["https://openalex.org/I41641357"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"\u0130pek Sar\u0131bal","raw_affiliation_strings":["Ege University","Faculty of Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ege University","institution_ids":["https://openalex.org/I41641357"]},{"raw_affiliation_string":"Faculty of Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5159232585","display_name":"Asude Sezer","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I41641357","display_name":"Ege University","ror":"https://ror.org/02eaafc18","country_code":"TR","type":"education","lineage":["https://openalex.org/I41641357"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Asude Sezer","raw_affiliation_strings":["Ege University","Faculty of Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ege University","institution_ids":["https://openalex.org/I41641357"]},{"raw_affiliation_string":"Faculty of Engineering","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002077332","display_name":"S\u00fcleyman Selim \u00c7\u0131naro\u011flu","orcid":"https://orcid.org/0000-0001-7120-3540","observed_orcids":["https://orcid.org/0000-0001-7120-3540"]},"institutions":[{"id":"https://openalex.org/I41641357","display_name":"Ege University","ror":"https://ror.org/02eaafc18","country_code":"TR","type":"education","lineage":["https://openalex.org/I41641357"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Suleyman Selim Cinaroglu","raw_affiliation_strings":["\u2020Department of Bioengineering , Faculty of Engineering , Ege University , \u0130zmir , T\u00fcrkiye"],"raw_orcid":"https://orcid.org/0000-0001-7120-3540","affiliations":[{"raw_affiliation_string":"\u2020Department of Bioengineering , Faculty of Engineering , Ege University , \u0130zmir , T\u00fcrkiye","institution_ids":["https://openalex.org/I41641357"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I41641357"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.649399995803833,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.649399995803833,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.125,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12534","display_name":"Protein Degradation and Inhibitors","score":0.06080000102519989,"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/bromodomain","display_name":"bromodomain","score":0.7089999914169312},{"id":"https://openalex.org/keywords/absolute-binding-free-energy","display_name":"absolute binding free energy","score":0.9639999866485596},{"id":"https://openalex.org/keywords/water-model","display_name":"water model","score":0.6949999928474426},{"id":"https://openalex.org/keywords/tip3p-water-model","display_name":"TIP3P water model","score":0.9419999718666077},{"id":"https://openalex.org/keywords/tip4p","display_name":"TIP4P","score":0.9589999914169312},{"id":"https://openalex.org/keywords/tip5p","display_name":"TIP5P","score":0.9950000047683716},{"id":"https://openalex.org/keywords/alchemical-free-energy-calculations","display_name":"alchemical free energy calculations","score":0.5770000219345093},{"id":"https://openalex.org/keywords/binding-affinity-prediction","display_name":"binding affinity prediction","score":0.628000020980835},{"id":"https://openalex.org/keywords/solvent-effects","display_name":"solvent effects","score":0.3449999988079071},{"id":"https://openalex.org/keywords/finite-size-corrections","display_name":"finite-size corrections","score":0.5839999914169312},{"id":"https://openalex.org/keywords/charged-ligands","display_name":"charged ligands","score":0.7149999737739563}],"concepts":[{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.7358999848365784},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6748999953269958},{"id":"https://openalex.org/C156911925","wikidata":"https://www.wikidata.org/wiki/Q643384","display_name":"Isothermal titration calorimetry","level":2,"score":0.656000018119812},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.5537999868392944},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.4666999876499176},{"id":"https://openalex.org/C133347239","wikidata":"https://www.wikidata.org/wiki/Q486921","display_name":"Isothermal process","level":2,"score":0.40400001406669617},{"id":"https://openalex.org/C2779455329","wikidata":"https://www.wikidata.org/wiki/Q22908915","display_name":"Solvent models","level":4,"score":0.3752000033855438},{"id":"https://openalex.org/C2780471494","wikidata":"https://www.wikidata.org/wiki/Q146505","display_name":"Solvent","level":2,"score":0.33709999918937683},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.3287000060081482},{"id":"https://openalex.org/C188154048","wikidata":"https://www.wikidata.org/wiki/Q6803609","display_name":"Mean absolute error","level":3,"score":0.3264999985694885},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.3237000107765198},{"id":"https://openalex.org/C202270520","wikidata":"https://www.wikidata.org/wiki/Q634314","display_name":"Calorimetry","level":2,"score":0.32089999318122864},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3138999938964844},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.30709999799728394},{"id":"https://openalex.org/C119049451","wikidata":"https://www.wikidata.org/wiki/Q3318070","display_name":"Water model","level":3,"score":0.3057999908924103},{"id":"https://openalex.org/C51329190","wikidata":"https://www.wikidata.org/wiki/Q1076349","display_name":"Ising model","level":2,"score":0.3003999888896942},{"id":"https://openalex.org/C184866935","wikidata":"https://www.wikidata.org/wiki/Q191010","display_name":"Titration","level":2,"score":0.29499998688697815},{"id":"https://openalex.org/C2780813799","wikidata":"https://www.wikidata.org/wiki/Q3274237","display_name":"Zero (linguistics)","level":2,"score":0.29440000653266907},{"id":"https://openalex.org/C22499117","wikidata":"https://www.wikidata.org/wiki/Q2253702","display_name":"Interaction energy","level":3,"score":0.2858000099658966},{"id":"https://openalex.org/C141780669","wikidata":"https://www.wikidata.org/wiki/Q7783161","display_name":"Thermodynamic integration","level":3,"score":0.2847999930381775},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.2773999869823456},{"id":"https://openalex.org/C166950319","wikidata":"https://www.wikidata.org/wiki/Q245031","display_name":"Intermolecular force","level":3,"score":0.25769999623298645},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.25609999895095825},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.25429999828338623},{"id":"https://openalex.org/C97514900","wikidata":"https://www.wikidata.org/wiki/Q719597","display_name":"Energetics","level":2,"score":0.2542000114917755}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.26434/chemrxiv.15010882/v1","doi":"https://doi.org/10.26434/chemrxiv.15010882/v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.15010882/v1","pdf_url":"https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15010882/v1","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":null,"raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.26434/chemrxiv.15010882/v1","doi":"https://doi.org/10.26434/chemrxiv.15010882/v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.15010882/v1","pdf_url":"https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15010882/v1","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320317245","display_name":"Ulusal Y\u00fcksek Ba\u015far\u0131ml\u0131 Hesaplama Merkezi, Istanbul Teknik \u00dcniversitesi","ror":"https://ror.org/03hx70339"},{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7223180932.pdf","grobid_xml":"https://content.openalex.org/works/W7223180932.grobid-xml"},"referenced_works_count":82,"referenced_works":["https://openalex.org/W312927025","https://openalex.org/W1031578623","https://openalex.org/W1928502853","https://openalex.org/W1974631163","https://openalex.org/W1976499671","https://openalex.org/W1978393297","https://openalex.org/W1981225934","https://openalex.org/W1988037271","https://openalex.org/W1997562335","https://openalex.org/W2015688756","https://openalex.org/W2015914415","https://openalex.org/W2020357919","https://openalex.org/W2020804982","https://openalex.org/W2024726841","https://openalex.org/W2024762727","https://openalex.org/W2037535298","https://openalex.org/W2037896546","https://openalex.org/W2041535798","https://openalex.org/W2043383571","https://openalex.org/W2063456921","https://openalex.org/W2066690664","https://openalex.org/W2072604508","https://openalex.org/W2087596773","https://openalex.org/W2103034037","https://openalex.org/W2118428599","https://openalex.org/W2123647733","https://openalex.org/W2127322768","https://openalex.org/W2147993766","https://openalex.org/W2151022427","https://openalex.org/W2210685190","https://openalex.org/W2302459535","https://openalex.org/W2330799739","https://openalex.org/W2343608145","https://openalex.org/W2404280981","https://openalex.org/W2513727910","https://openalex.org/W2518483157","https://openalex.org/W2531288146","https://openalex.org/W2560915683","https://openalex.org/W2618361354","https://openalex.org/W2731784911","https://openalex.org/W2743262308","https://openalex.org/W2766288270","https://openalex.org/W2768709305","https://openalex.org/W2772606519","https://openalex.org/W2803653576","https://openalex.org/W2886540393","https://openalex.org/W2900679912","https://openalex.org/W2935752271","https://openalex.org/W2944366462","https://openalex.org/W2952635193","https://openalex.org/W2989052455","https://openalex.org/W3008665460","https://openalex.org/W3047663514","https://openalex.org/W3121466164","https://openalex.org/W3121733667","https://openalex.org/W3138474425","https://openalex.org/W3163631242","https://openalex.org/W3193536562","https://openalex.org/W3200958602","https://openalex.org/W3203204467","https://openalex.org/W3208130945","https://openalex.org/W3210641718","https://openalex.org/W4220686399","https://openalex.org/W4224216258","https://openalex.org/W4294679529","https://openalex.org/W4309089104","https://openalex.org/W4317360676","https://openalex.org/W4318019007","https://openalex.org/W4372332985","https://openalex.org/W4376870323","https://openalex.org/W4379179528","https://openalex.org/W4387164156","https://openalex.org/W4393680772","https://openalex.org/W4394694796","https://openalex.org/W4399611311","https://openalex.org/W4402674041","https://openalex.org/W4403223960","https://openalex.org/W4404458588","https://openalex.org/W4405438726","https://openalex.org/W4408804342","https://openalex.org/W4416839980","https://openalex.org/W7119530797"],"related_works":["https://openalex.org/W7096015154","https://openalex.org/W3183237657","https://openalex.org/W2031888811","https://openalex.org/W2618361354","https://openalex.org/W1991658959","https://openalex.org/W2318468182","https://openalex.org/W2805498355","https://openalex.org/W4254402718","https://openalex.org/W2743262308","https://openalex.org/W2566391875"],"abstract_inverted_index":{"The":[0,104,165],"choice":[1],"of":[2,27,98,101],"explicit":[3],"water":[4,42],"model":[5],"may":[6],"affect":[7],"absolute":[8],"binding":[9,185],"free":[10],"energy":[11],"(ABFE)":[12],"predictions":[13],"for":[14,70,161,207],"bromodomains,":[15],"whose":[16],"conserved":[17],"acetyl-lysine":[18],"pockets":[19],"contain":[20],"structured":[21],"waters.":[22],"We":[23],"assembled":[24],"a":[25,50,115],"benchmark":[26,127],"ten":[28],"distinct":[29],"bromodomain\u2013ligand":[30],"complexes":[31],"with":[32,81,203],"experimental":[33,88],"isothermal":[34],"titration":[35],"calorimetry":[36],"thermodynamics":[37],"and":[38,47,112,171,192],"compared":[39],"four":[40,145],"TIP-family":[41],"models,":[43,73],"TIP3P,":[44],"TIP4P,":[45],"TIP5P,":[46],"TIP7P,":[48],"using":[49],"common":[51],"alchemical":[52],"protocol.":[53],"TIP3P":[54,111],"gave":[55,198],"the":[56,71,75,87,96,99,102,126,134,144,162,183,194,210],"lowest":[57,76],"point-estimate":[58],"mean":[59],"unsigned":[60],"error":[61],"(MUE),":[62],"1.56":[63],"kcal":[64,68,93,106],"mol\u22121,":[65,94],"against":[66],"1.89\u20132.11":[67],"mol\u22121":[69,107],"other":[72,152],"at":[74],"cost.":[77,211],"TIP7P":[78,113],"correlated":[79],"best":[80],"experiment":[82],"(r":[83],"=":[84],"0.73),":[85],"but":[86,131],"affinities":[89,136],"span":[90],"only":[91,125],"2.1":[92],"about":[95],"size":[97],"errors":[100],"models.":[103],"0.55":[105],"MUE":[108],"difference":[109,154],"between":[110],"had":[114],"nominal":[116],"95%":[117],"paired":[118,153],"bootstrap":[119],"interval":[120],"that":[121,169],"excluded":[122],"zero":[123],"when":[124,133],"composition":[128],"was":[129,155],"resampled,":[130],"not":[132],"calculated":[135],"were":[137,148],"perturbed":[138],"by":[139],"their":[140],"sampling-sensitivity":[141],"measures":[142],"or":[143],"charged":[146,163],"ligands":[147],"left":[149],"out.":[150],"No":[151],"resolved,":[156],"including":[157],"after":[158],"finite-size":[159],"corrections":[160],"ligands.":[164],"leg":[166],"decomposition":[167],"shows":[168],"solvent":[170],"complex":[172,191],"contributions":[173],"can":[174],"compensate,":[175],"so":[176],"water-model":[177],"effects":[178],"must":[179],"be":[180],"judged":[181],"over":[182],"complete":[184],"cycle.":[186],"With":[187],"one":[188],"calculation":[189],"per":[190],"model,":[193],"higher-site":[195],"TIP":[196],"models":[197],"no":[199],"demonstrated":[200],"accuracy":[201],"benefit":[202],"this":[204],"force":[205],"field":[206],"1.4\u20132.7":[208],"times":[209]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-10-22T00:00:00"}
