{"id":"https://openalex.org/W4386439097","doi":"https://doi.org/10.1002/pmic.202300219","title":"Prediction of protein interactions is essential for studying biomolecular mechanisms","display_name":"Prediction of protein interactions is essential for studying biomolecular mechanisms","publication_year":2023,"publication_date":"2023-09-01","ids":{"openalex":"https://openalex.org/W4386439097","doi":"https://doi.org/10.1002/pmic.202300219","pmid":"https://pubmed.ncbi.nlm.nih.gov/37667816"},"language":"en","primary_location":{"id":"doi:10.1002/pmic.202300219","doi":"https://doi.org/10.1002/pmic.202300219","is_oa":false,"landing_page_url":"https://doi.org/10.1002/pmic.202300219","pdf_url":null,"source":{"id":"https://openalex.org/S182655450","display_name":"PROTEOMICS","issn_l":"1615-9853","issn":["1615-9853","1615-9861"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PROTEOMICS","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.authorea.com/doi/pdf/10.22541/au.168813185.58433396","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013394507","display_name":"Ilya A. Vakser","orcid":"https://orcid.org/0000-0002-5743-2934","observed_orcids":["https://orcid.org/0000-0002-5743-2934"]},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ilya A. Vakser","raw_affiliation_strings":["Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA"],"raw_orcid":"https://orcid.org/0000-0002-5743-2934","affiliations":[{"raw_affiliation_string":"Computational Biology Program, The University of Kansas, Lawrence, Kansas, USA","institution_ids":["https://openalex.org/I146416000"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5013394507"],"corresponding_institution_ids":["https://openalex.org/I146416000"],"apc_list":{"value":4220,"currency":"USD","value_usd":4220},"apc_paid":null,"fwci":0.1545,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.34588058,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":95},"biblio":{"volume":"23","issue":"17","first_page":"e2300219","last_page":"e2300219"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9067000150680542,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9067000150680542,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.05869999900460243,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.010200000368058681,"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/protein-protein-interaction","display_name":"protein-protein interaction","score":0.906000018119812},{"id":"https://openalex.org/keywords/benchmark-dataset","display_name":"benchmark dataset","score":0.6859999895095825},{"id":"https://openalex.org/keywords/scoring-functions","display_name":"scoring functions","score":0.8539999723434448},{"id":"https://openalex.org/keywords/alphafold","display_name":"AlphaFold","score":0.8009999990463257},{"id":"https://openalex.org/keywords/deep-learning","display_name":"deep learning","score":0.6690000295639038},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"protein structure prediction","score":0.7440000176429749},{"id":"https://openalex.org/keywords/protein-complex-modeling","display_name":"protein complex modeling","score":0.3529999852180481}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6058964729309082},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5553097128868103},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5427359342575073},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.5037955641746521},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5032784342765808},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4790043532848358},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.4600932002067566},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.44821470975875854},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4386165738105774},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3597816228866577},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.325247585773468},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32478708028793335},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32249265909194946},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12361150979995728},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1002/pmic.202300219","doi":"https://doi.org/10.1002/pmic.202300219","is_oa":false,"landing_page_url":"https://doi.org/10.1002/pmic.202300219","pdf_url":null,"source":{"id":"https://openalex.org/S182655450","display_name":"PROTEOMICS","issn_l":"1615-9853","issn":["1615-9853","1615-9861"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PROTEOMICS","raw_type":"journal-article"},{"id":"doi:10.22541/au.168813185.58433396/v1","doi":"https://doi.org/10.22541/au.168813185.58433396/v1","is_oa":true,"landing_page_url":"https://doi.org/10.22541/au.168813185.58433396/v1","pdf_url":"https://www.authorea.com/doi/pdf/10.22541/au.168813185.58433396","source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"pmid:37667816","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37667816","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,"listed_in":[],"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":"Proteomics","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.22541/au.168813185.58433396/v1","doi":"https://doi.org/10.22541/au.168813185.58433396/v1","is_oa":true,"landing_page_url":"https://doi.org/10.22541/au.168813185.58433396/v1","pdf_url":"https://www.authorea.com/doi/pdf/10.22541/au.168813185.58433396","source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386439097.pdf","grobid_xml":"https://content.openalex.org/works/W4386439097.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2000383223","https://openalex.org/W2024911966","https://openalex.org/W2155796229","https://openalex.org/W2163614321","https://openalex.org/W2937282616","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3202105508","https://openalex.org/W4213446001","https://openalex.org/W4296060337","https://openalex.org/W4300594517","https://openalex.org/W4315432725","https://openalex.org/W4382181821"],"related_works":["https://openalex.org/W4382181821","https://openalex.org/W7100353896","https://openalex.org/W2118787503","https://openalex.org/W7099486595","https://openalex.org/W7164557288","https://openalex.org/W2123583836","https://openalex.org/W2778072166","https://openalex.org/W4387561381","https://openalex.org/W3135883064","https://openalex.org/W4212980571"],"abstract_inverted_index":{"Structural":[0],"characterization":[1],"of":[2,20,30,42,60,72,76,97,108,126,141,169,172],"protein":[3,21,43],"interactions":[4,44],"is":[5,133,176],"essential":[6],"for":[7,192],"our":[8],"ability":[9,118,159],"to":[10,18,119,138,160],"understand":[11],"and":[12,40,91,99,103,185,194],"modulate":[13],"physiological":[14,78,98,128],"processes.":[15],"Computational":[16],"approaches":[17],"modeling":[19],"complexes":[22],"provide":[23],"structural":[24],"information":[25],"that":[26],"far":[27],"exceeds":[28],"capabilities":[29],"the":[31,51,121,139,146,158,167],"existing":[32],"experimental":[33],"techniques.":[34,57],"Protein":[35],"structure":[36],"prediction":[37,41],"in":[38,45,54,149,166,188],"general,":[39],"particular,":[46],"has":[47],"been":[48],"revolutionized":[49],"by":[50],"rapid":[52],"progress":[53],"Deep":[55],"Learning":[56],"The":[58,88,124,178],"work":[59],"Schweke":[61],"et":[62],"al.":[63],"(Proteomics":[64],"2023,":[65],"23,":[66],"2200323)":[67],"presents":[68,180],"a":[69,93,105,142,150,154,173,181],"community-wide":[70],"study":[71,179],"an":[73],"important":[74,190],"problem":[75,125],"distinguishing":[77],"protein-protein":[79,174],"complexes/interfaces":[80],"(experimentally":[81],"determined":[82],"or":[83],"modeled)":[84],"from":[85,130],"non-physiological":[86,100,122,131],"ones.":[87],"authors":[89],"designed":[90],"generated":[92],"large":[94,106],"benchmark":[95],"set":[96,107],"homodimeric":[101],"complexes,":[102],"evaluated":[104],"scoring":[109],"functions,":[110],"as":[111,113],"well":[112],"AlphaFold":[114],"predictions,":[115],"on":[116],"their":[117],"discriminate":[120],"interfaces.":[123],"separating":[127],"interfaces":[129,165],"ones":[132],"very":[134],"difficult,":[135],"largely":[136],"due":[137],"lack":[140],"clear":[143],"distinction":[144],"between":[145],"two":[147],"categories":[148],"crowded":[151],"environment":[152],"inside":[153],"living":[155],"cell.":[156],"Still,":[157],"identify":[161],"key":[162],"physiologically":[163],"significant":[164],"variety":[168],"possible":[170],"configurations":[171],"complex":[175],"important.":[177],"major":[182],"data":[183],"resource":[184],"methodological":[186],"development":[187],"this":[189],"direction":[191],"molecular":[193],"cellular":[195],"biology.":[196]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2023-09-06T00:00:00"}