{"id":"https://openalex.org/W4413039342","doi":"https://doi.org/10.1021/acs.jcim.5c00838","title":"MPLBind: Predicting the Effect of Binding Site Point Mutations on Protein\u2013Ligand Binding Affinity Using Protein Large Language Models","display_name":"MPLBind: Predicting the Effect of Binding Site Point Mutations on Protein\u2013Ligand Binding Affinity Using Protein Large Language Models","publication_year":2025,"publication_date":"2025-08-07","ids":{"openalex":"https://openalex.org/W4413039342","doi":"https://doi.org/10.1021/acs.jcim.5c00838","pmid":"https://pubmed.ncbi.nlm.nih.gov/40772546"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00838","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00838","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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/A5001745410","display_name":"Jiahuan Jin","orcid":"https://orcid.org/0000-0002-9637-5450"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["CN","IN"],"is_corresponding":false,"raw_author_name":"Jiahuan Jin","raw_affiliation_strings":["Harbin Institute of Technology","Research Center of Bioinformatics, School of Computer Science and Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Harbin Institute of Technology","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"Research Center of Bioinformatics, School of Computer Science and Technology","institution_ids":["https://openalex.org/I4210148697"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066052627","display_name":"Jie Li","orcid":"https://orcid.org/0000-0001-9359-3586"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I4210148697","display_name":"Institute of Bioinformatics","ror":"https://ror.org/04hqfvm50","country_code":"IN","type":"nonprofit","lineage":["https://openalex.org/I4210148697"]}],"countries":["CN","IN"],"is_corresponding":true,"raw_author_name":"Jie Li","raw_affiliation_strings":["Harbin Institute of Technology","Research Center of Bioinformatics, School of Computer Science and Technology"],"raw_orcid":"https://orcid.org/0000-0001-9359-3586","affiliations":[{"raw_affiliation_string":"Harbin Institute of Technology","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"Research Center of Bioinformatics, School of Computer Science and Technology","institution_ids":["https://openalex.org/I4210148697"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5066052627"],"corresponding_institution_ids":["https://openalex.org/I204983213","https://openalex.org/I4210148697"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.20558317,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"65","issue":"16","first_page":"8720","last_page":"8729"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987999796867371,"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":0.9987999796867371,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9962999820709229,"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":0.9959999918937683,"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/point-mutation","display_name":"Point mutation","score":0.5788857936859131},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5242738723754883},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.519027829170227},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.452900767326355},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.440584659576416},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.362165629863739},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.332897424697876},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3261467218399048},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25700223445892334},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.1622278392314911},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12053769826889038}],"concepts":[{"id":"https://openalex.org/C176944494","wikidata":"https://www.wikidata.org/wiki/Q1415380","display_name":"Point mutation","level":4,"score":0.5788857936859131},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5242738723754883},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.519027829170227},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.452900767326355},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.440584659576416},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.362165629863739},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.332897424697876},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3261467218399048},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25700223445892334},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.1622278392314911},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12053769826889038}],"mesh":[{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","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":"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":"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":"D008958","descriptor_name":"Models, Molecular","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c00838","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00838","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40772546","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40772546","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 chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7705019297","display_name":null,"funder_award_id":"62372134","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"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1619777468","https://openalex.org/W1982467516","https://openalex.org/W2035585923","https://openalex.org/W2068167378","https://openalex.org/W2086286404","https://openalex.org/W2092285329","https://openalex.org/W2105803236","https://openalex.org/W2114850508","https://openalex.org/W2134967712","https://openalex.org/W2157760740","https://openalex.org/W2467199644","https://openalex.org/W2622236128","https://openalex.org/W2785947426","https://openalex.org/W2912083425","https://openalex.org/W2935161127","https://openalex.org/W2951885137","https://openalex.org/W3007942792","https://openalex.org/W3014696958","https://openalex.org/W3019745511","https://openalex.org/W3167575787","https://openalex.org/W3177500196","https://openalex.org/W3201360810","https://openalex.org/W3208254245","https://openalex.org/W4205773061","https://openalex.org/W4221070434","https://openalex.org/W4296162381","https://openalex.org/W4308142437","https://openalex.org/W4308834893","https://openalex.org/W4318981550","https://openalex.org/W4319923818","https://openalex.org/W4322776009","https://openalex.org/W4365508870","https://openalex.org/W4380683039","https://openalex.org/W4380739447","https://openalex.org/W4385351607","https://openalex.org/W4389836921","https://openalex.org/W4399011591","https://openalex.org/W4403514887","https://openalex.org/W4408144058"],"related_works":["https://openalex.org/W2550943714","https://openalex.org/W3212350425","https://openalex.org/W2388007221","https://openalex.org/W2511508046","https://openalex.org/W1974452506","https://openalex.org/W2363458739","https://openalex.org/W2385244308","https://openalex.org/W2028961943","https://openalex.org/W2025584407","https://openalex.org/W2375287167"],"abstract_inverted_index":{"Protein-ligand":[0],"binding":[1,15,40,45,74,145,157],"affinity":[2,146],"may":[3,18],"be":[4],"affected":[5],"by":[6],"protein":[7,90,104,111],"mutations,":[8],"especially":[9],"point":[10],"mutations":[11,42,51,71,154],"occurring":[12],"within":[13],"the":[14,37,48,68,109,115,125,151],"site,":[16],"which":[17,76,94],"indirectly":[19],"contribute":[20],"to":[21,35,54,66],"interindividual":[22],"differences":[23],"in":[24,142,149],"drug":[25],"response.":[26],"In":[27,57],"recent":[28],"years,":[29],"several":[30],"methods":[31],"have":[32],"been":[33],"proposed":[34,65],"predict":[36,55,67],"effect":[38,69,152],"of":[39,50,70,108,118,153],"site":[41],"on":[43,72,103,155],"protein-ligand":[44,73,144,156],"affinity.":[46,158],"However,":[47],"impact":[49],"is":[52,64],"difficult":[53],"accurately.":[56],"this":[58],"study,":[59],"a":[60],"method":[61],"named":[62],"MPLBind":[63,132],"affinity,":[75],"effectively":[77],"utilizes":[78],"ligand":[79,119],"descriptors":[80],"and":[81,88,100,114,120],"fingerprints,":[82],"mutant":[83],"residues'":[84],"local":[85],"environment":[86],"changes,":[87],"large":[89,110],"language":[91,112],"model":[92,113],"features,":[93],"contain":[95],"context,":[96],"evolutionary":[97],"information,":[98],"conservation,":[99],"functional":[101],"information":[102],"sequences.":[105],"The":[106],"use":[107],"fusion":[116],"strategy":[117],"mutation":[121],"features":[122],"significantly":[123],"improved":[124],"prediction":[126],"performance.":[127],"Experimental":[128],"results":[129],"show":[130],"that":[131],"has":[133],"better":[134],"performance":[135],"against":[136],"competing":[137],"baseline":[138],"models,":[139],"not":[140],"only":[141],"predicting":[143,150],"but":[147],"also":[148]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}