{"id":"https://openalex.org/W4406658272","doi":"https://doi.org/10.1109/tcbbio.2025.3532332","title":"Enhancing Chemical Prediction in Plasma Protein Binding: A Deep Learning Model Combining Molecular Descriptors and Fingerprint Representation With Attention Mechanisms","display_name":"Enhancing Chemical Prediction in Plasma Protein Binding: A Deep Learning Model Combining Molecular Descriptors and Fingerprint Representation With Attention Mechanisms","publication_year":2025,"publication_date":"2025-01-21","ids":{"openalex":"https://openalex.org/W4406658272","doi":"https://doi.org/10.1109/tcbbio.2025.3532332","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811414"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3532332","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3532332","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","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/A5025364589","display_name":"Qifeng Tian","orcid":"https://orcid.org/0000-0002-4889-5371"},"institutions":[{"id":"https://openalex.org/I118803816","display_name":"Liaoning University","ror":"https://ror.org/03xpwj629","country_code":"CN","type":"education","lineage":["https://openalex.org/I118803816"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qifeng Tian","raw_affiliation_strings":["School of Life Science, Liaoning University, Shenyang, China"],"affiliations":[{"raw_affiliation_string":"School of Life Science, Liaoning University, Shenyang, China","institution_ids":["https://openalex.org/I118803816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108432409","display_name":"Jian Zhao","orcid":"https://orcid.org/0000-0002-9607-2337"},"institutions":[{"id":"https://openalex.org/I118803816","display_name":"Liaoning University","ror":"https://ror.org/03xpwj629","country_code":"CN","type":"education","lineage":["https://openalex.org/I118803816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Zhao","raw_affiliation_strings":["School of Life Science, Liaoning University, Shenyang, China"],"affiliations":[{"raw_affiliation_string":"School of Life Science, Liaoning University, Shenyang, China","institution_ids":["https://openalex.org/I118803816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101723104","display_name":"Zhe He","orcid":"https://orcid.org/0000-0002-7527-9160"},"institutions":[{"id":"https://openalex.org/I118803816","display_name":"Liaoning University","ror":"https://ror.org/03xpwj629","country_code":"CN","type":"education","lineage":["https://openalex.org/I118803816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhe He","raw_affiliation_strings":["School of Life Science, Liaoning University, Shenyang, China"],"affiliations":[{"raw_affiliation_string":"School of Life Science, Liaoning University, Shenyang, China","institution_ids":["https://openalex.org/I118803816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028136435","display_name":"Jinhui Meng","orcid":"https://orcid.org/0000-0003-4234-6440"},"institutions":[{"id":"https://openalex.org/I118803816","display_name":"Liaoning University","ror":"https://ror.org/03xpwj629","country_code":"CN","type":"education","lineage":["https://openalex.org/I118803816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinhui Meng","raw_affiliation_strings":["School of Life Science, Liaoning University, Shenyang, China"],"affiliations":[{"raw_affiliation_string":"School of Life Science, Liaoning University, Shenyang, China","institution_ids":["https://openalex.org/I118803816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017208665","display_name":"Xiaoyu Liu","orcid":"https://orcid.org/0000-0001-5928-0244"},"institutions":[{"id":"https://openalex.org/I118803816","display_name":"Liaoning University","ror":"https://ror.org/03xpwj629","country_code":"CN","type":"education","lineage":["https://openalex.org/I118803816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyu Liu","raw_affiliation_strings":["School of Life Science, Liaoning University, Shenyang, China"],"affiliations":[{"raw_affiliation_string":"School of Life Science, Liaoning University, Shenyang, China","institution_ids":["https://openalex.org/I118803816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113402827","display_name":"Mengfeng Hu","orcid":"https://orcid.org/0009-0001-3267-5921"},"institutions":[{"id":"https://openalex.org/I118803816","display_name":"Liaoning University","ror":"https://ror.org/03xpwj629","country_code":"CN","type":"education","lineage":["https://openalex.org/I118803816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengfeng Hu","raw_affiliation_strings":["School of Life Science, Liaoning University, Shenyang, China"],"affiliations":[{"raw_affiliation_string":"School of Life Science, Liaoning University, Shenyang, China","institution_ids":["https://openalex.org/I118803816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059943654","display_name":"Jinhan Liu","orcid":"https://orcid.org/0000-0002-3092-7021"},"institutions":[{"id":"https://openalex.org/I118803816","display_name":"Liaoning University","ror":"https://ror.org/03xpwj629","country_code":"CN","type":"education","lineage":["https://openalex.org/I118803816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinhan Liu","raw_affiliation_strings":["School of Life Science, Liaoning University, Shenyang, China"],"affiliations":[{"raw_affiliation_string":"School of Life Science, Liaoning University, Shenyang, China","institution_ids":["https://openalex.org/I118803816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028502785","display_name":"Huawei Feng","orcid":"https://orcid.org/0000-0002-3494-4590"},"institutions":[{"id":"https://openalex.org/I118803816","display_name":"Liaoning University","ror":"https://ror.org/03xpwj629","country_code":"CN","type":"education","lineage":["https://openalex.org/I118803816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huawei Feng","raw_affiliation_strings":["School of Pharmacy, Liaoning University, Shenyang, China"],"affiliations":[{"raw_affiliation_string":"School of Pharmacy, Liaoning University, Shenyang, China","institution_ids":["https://openalex.org/I118803816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100425398","display_name":"Li Zhang","orcid":"https://orcid.org/0000-0001-5029-2134"},"institutions":[{"id":"https://openalex.org/I118803816","display_name":"Liaoning University","ror":"https://ror.org/03xpwj629","country_code":"CN","type":"education","lineage":["https://openalex.org/I118803816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Zhang","raw_affiliation_strings":["School of Life Science, Liaoning University, Shenyang, China"],"affiliations":[{"raw_affiliation_string":"School of Life Science, Liaoning University, Shenyang, China","institution_ids":["https://openalex.org/I118803816"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100338910","display_name":"Hongsheng Liu","orcid":"https://orcid.org/0000-0001-9242-6508"},"institutions":[{"id":"https://openalex.org/I118803816","display_name":"Liaoning University","ror":"https://ror.org/03xpwj629","country_code":"CN","type":"education","lineage":["https://openalex.org/I118803816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongsheng Liu","raw_affiliation_strings":["School of Pharmacy, Liaoning University, Shenyang, China"],"affiliations":[{"raw_affiliation_string":"School of Pharmacy, Liaoning University, Shenyang, China","institution_ids":["https://openalex.org/I118803816"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5025364589"],"corresponding_institution_ids":["https://openalex.org/I118803816"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.01005534,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"2","first_page":"653","last_page":"660"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9674999713897705,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9674999713897705,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.920199990272522,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6917977333068848},{"id":"https://openalex.org/keywords/fingerprint","display_name":"Fingerprint (computing)","score":0.6348495483398438},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5559914112091064},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42612335085868835},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3543311655521393},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32546404004096985}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6917977333068848},{"id":"https://openalex.org/C2777826928","wikidata":"https://www.wikidata.org/wiki/Q3745713","display_name":"Fingerprint (computing)","level":2,"score":0.6348495483398438},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5559914112091064},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42612335085868835},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3543311655521393},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32546404004096985},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3532332","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3532332","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811414","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811414","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1738141789","display_name":null,"funder_award_id":"JYTQN2023187","funder_id":"https://openalex.org/F4320324560","funder_display_name":"Department of Education of Liaoning Province"},{"id":"https://openalex.org/G2444866926","display_name":null,"funder_award_id":"RC220277","funder_id":"https://openalex.org/F4320336621","funder_display_name":"Shenyang Young and Middle-aged Science and Technology Innovation Talent Support Program"},{"id":"https://openalex.org/G2672728137","display_name":null,"funder_award_id":"RC210216","funder_id":"https://openalex.org/F4320336621","funder_display_name":"Shenyang Young and Middle-aged Science and Technology Innovation Talent Support Program"},{"id":"https://openalex.org/G8724762027","display_name":null,"funder_award_id":"LJKMZ20220455","funder_id":"https://openalex.org/F4320324560","funder_display_name":"Department of Education of Liaoning Province"},{"id":"https://openalex.org/G8736110462","display_name":null,"funder_award_id":"82003655","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324560","display_name":"Department of Education of Liaoning Province","ror":"https://ror.org/0022v2454"},{"id":"https://openalex.org/F4320336621","display_name":"Shenyang Young and Middle-aged Science and Technology Innovation Talent Support Program","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W43382659","https://openalex.org/W87190817","https://openalex.org/W964460774","https://openalex.org/W1009394721","https://openalex.org/W1876084227","https://openalex.org/W1975147762","https://openalex.org/W2008056655","https://openalex.org/W2016023958","https://openalex.org/W2027666102","https://openalex.org/W2034705752","https://openalex.org/W2038262677","https://openalex.org/W2097688080","https://openalex.org/W2102148524","https://openalex.org/W2160471073","https://openalex.org/W2221700889","https://openalex.org/W2405527140","https://openalex.org/W2766878249","https://openalex.org/W2781120690","https://openalex.org/W2900090807","https://openalex.org/W2905012389","https://openalex.org/W2959623824","https://openalex.org/W2959938226","https://openalex.org/W2968734407","https://openalex.org/W2997591727","https://openalex.org/W3004497899","https://openalex.org/W3040137644","https://openalex.org/W3107688684","https://openalex.org/W3124409690","https://openalex.org/W3165037864","https://openalex.org/W3199470976","https://openalex.org/W3202227570","https://openalex.org/W3208271237","https://openalex.org/W4220964139","https://openalex.org/W4243150065","https://openalex.org/W4280602833","https://openalex.org/W4281383202","https://openalex.org/W4293105114","https://openalex.org/W4297179162","https://openalex.org/W4313706848","https://openalex.org/W4319458186","https://openalex.org/W4323065323","https://openalex.org/W4385442674","https://openalex.org/W4403809075","https://openalex.org/W6683295017","https://openalex.org/W6742632731","https://openalex.org/W6749029207"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W2033914206"],"abstract_inverted_index":{"Plasma":[0],"protein":[1,52],"binding":[2,53],"(PPB)":[3],"is":[4,10],"an":[5,76,80,84,89,99,112],"important":[6,11],"pharmacokinetic":[7],"parameter.":[8],"It":[9],"to":[12,118,126,141],"measure":[13],"the":[14,94,120,144],"PPB":[15],"properties":[16],"of":[17,78,82,86,91],"drug":[18,21],"molecules":[19],"during":[20],"development.":[22],"However,":[23],"in":[24,27,33],"vivo":[25],"or":[26],"vitro":[28],"measurements":[29],"are":[30,37],"time-consuming.":[31],"Therefore,":[32],"silico":[34],"prediction":[35,54],"methods":[36],"promising":[38],"time-saving":[39],"alternatives.":[40],"This":[41],"study":[42],"presents":[43],"a":[44],"new":[45],"deep":[46],"learning":[47],"model":[48],"called":[49],"enhancing":[50],"plasma":[51],"(ePPBP)":[55],"that":[56,103],"merges":[57],"molecular":[58,60,105],"descriptors,":[59],"fingerprints":[61],"and":[62,88,133],"graph":[63],"features":[64],"for":[65],"predicting":[66],"PPB.":[67],"The":[68,130],"ePPBP":[69,109,123],"currently":[70],"has":[71],"state-of-the-art":[72],"(SOTA)":[73],"performance,":[74],"with":[75],"Rp<sup>2</sup>":[77],"0.8663,":[79],"R<sup>2</sup>":[81],"0.8630,":[83],"MAE":[85],"0.0613":[87],"RMSE":[90],"0.1041":[92],"on":[93],"test":[95],"set.":[96],"In":[97],"addition,":[98],"ablation":[100],"experiment":[101,115],"demonstrated":[102],"different":[104],"representations":[106],"can":[107],"improve":[108],"performance.":[110],"Next,":[111],"uncertainty":[113],"estimation":[114],"was":[116,124],"used":[117,125],"estimate":[119],"confidence":[121,139],"when":[122],"predict":[127],"unknown":[128],"chemicals.":[129],"MHFP":[131],"distance":[132],"RDKFP":[134],"similarity":[135],"were":[136,146],"selected":[137],"as":[138],"indicators":[140],"determine":[142],"whether":[143],"predictions":[145],"credible":[147],"from":[148],"ePPBP.":[149]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
