{"id":"https://openalex.org/W4406260355","doi":"https://doi.org/10.1109/bibm62325.2024.10822503","title":"Efficient Prediction of Protein-Ligand Binding Using ESM-2 and Mol2vec with Random Forest Model","display_name":"Efficient Prediction of Protein-Ligand Binding Using ESM-2 and Mol2vec with Random Forest Model","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406260355","doi":"https://doi.org/10.1109/bibm62325.2024.10822503"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822503","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822503","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5091622645","display_name":"Bichar Dip Shrestha Gurung","orcid":"https://orcid.org/0000-0002-9818-5108"},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bichar Dip Shrestha Gurung","raw_affiliation_strings":["University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA"],"affiliations":[{"raw_affiliation_string":"University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115840047","display_name":"Manish Rayamajhi","orcid":null},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manish Rayamajhi","raw_affiliation_strings":["University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA"],"affiliations":[{"raw_affiliation_string":"University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084219000","display_name":"Anushuya Baidya","orcid":"https://orcid.org/0000-0002-1613-9862"},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anushuya Baidya","raw_affiliation_strings":["University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA"],"affiliations":[{"raw_affiliation_string":"University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115840048","display_name":"Owen Growney","orcid":null},"institutions":[{"id":"https://openalex.org/I75350188","display_name":"Black Hills State University","ror":"https://ror.org/03fng6237","country_code":"US","type":"education","lineage":["https://openalex.org/I75350188"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Owen Growney","raw_affiliation_strings":["Black Hills State University,School of Natural Sciences,Spearfish,SD,USA"],"affiliations":[{"raw_affiliation_string":"Black Hills State University,School of Natural Sciences,Spearfish,SD,USA","institution_ids":["https://openalex.org/I75350188"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115840049","display_name":"Helena Naomie Dongmo Mafo","orcid":null},"institutions":[{"id":"https://openalex.org/I172980758","display_name":"Kennesaw State University","ror":"https://ror.org/00jeqjx33","country_code":"US","type":"education","lineage":["https://openalex.org/I172980758"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Helena Naomie Dongmo Mafo","raw_affiliation_strings":["Kennesaw State University,College of Computing and Software Engineering,Marietta,GA,USA"],"affiliations":[{"raw_affiliation_string":"Kennesaw State University,College of Computing and Software Engineering,Marietta,GA,USA","institution_ids":["https://openalex.org/I172980758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102826879","display_name":"Yun\u2010Seok Choi","orcid":"https://orcid.org/0000-0001-5102-123X"},"institutions":[{"id":"https://openalex.org/I75350188","display_name":"Black Hills State University","ror":"https://ror.org/03fng6237","country_code":"US","type":"education","lineage":["https://openalex.org/I75350188"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yun-Seok Choi","raw_affiliation_strings":["Black Hills State University,School of Natural Sciences,Spearfish,SD,USA"],"affiliations":[{"raw_affiliation_string":"Black Hills State University,School of Natural Sciences,Spearfish,SD,USA","institution_ids":["https://openalex.org/I75350188"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003549657","display_name":"Etienne Z. Gnimpi\u00e9ba","orcid":"https://orcid.org/0000-0002-5338-084X"},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Etienne Z. Gnimpieba","raw_affiliation_strings":["University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA"],"affiliations":[{"raw_affiliation_string":"University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA","institution_ids":["https://openalex.org/I189957204"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5091622645"],"corresponding_institution_ids":["https://openalex.org/I189957204"],"apc_list":null,"apc_paid":null,"fwci":0.3795,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.6850331,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"6893","last_page":"6895"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9797999858856201,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9797999858856201,"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/random-forest","display_name":"Random forest","score":0.8128934502601624},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5715804696083069},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3358571529388428},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.318167507648468}],"concepts":[{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.8128934502601624},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5715804696083069},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3358571529388428},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.318167507648468}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822503","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822503","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.44999998807907104,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320338440","display_name":"HORIZON EUROPE Health","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2038252445","https://openalex.org/W2096864392","https://openalex.org/W2777416523","https://openalex.org/W2785947426","https://openalex.org/W2809216727","https://openalex.org/W3029836473","https://openalex.org/W4283259285","https://openalex.org/W4307479771","https://openalex.org/W4327550249","https://openalex.org/W4388158819","https://openalex.org/W6871933655"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"In":[0],"this":[1],"study,":[2],"we":[3],"present":[4],"a":[5,19,65],"predictive":[6,62],"model":[7,83],"for":[8,102],"protein-ligand":[9],"binding":[10,106],"interactions,":[11],"leveraging":[12],"ESM-2":[13],"and":[14,34,43,56,64,81,104],"Mol2vec":[15],"embeddings":[16],"combined":[17],"with":[18,97],"Random":[20],"Forest":[21],"classifier.":[22],"Our":[23,87],"approach":[24],"was":[25,74],"evaluated":[26],"across":[27],"three":[28],"testing":[29],"scenarios\u2014\"Molecule":[30],"unseen,\"":[31,33],"\"Protein":[32],"\"None":[35],"seen\"\u2014to":[36],"assess":[37],"its":[38],"generalizability":[39],"to":[40,46,77],"novel":[41],"compounds":[42],"targets.":[44],"Compared":[45],"deep":[47],"learning":[48,100],"models,":[49],"our":[50],"method":[51],"demonstrated":[52],"competitive":[53],"AUROC":[54],"scores":[55],"consistently":[57],"high":[58],"specificity,":[59],"indicating":[60],"robust":[61],"performance":[63],"conservative":[66],"strategy":[67],"that":[68],"minimizes":[69],"false":[70],"positives.":[71],"While":[72],"sensitivity":[73,84],"lower,":[75],"strategies":[76],"address":[78],"data":[79],"imbalance":[80],"enhance":[82],"are":[85],"discussed.":[86],"findings":[88],"highlight":[89],"the":[90],"potential":[91],"of":[92],"combining":[93],"efficient":[94],"embedding":[95],"techniques":[96],"interpretable":[98],"machine":[99],"models":[101],"scalable":[103],"effective":[105],"interaction":[107],"prediction":[108]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2025-12-27T23:08:20.325037","created_date":"2025-10-10T00:00:00"}
