{"id":"https://openalex.org/W4386083644","doi":"https://doi.org/10.1093/bib/bbad299","title":"PredLLPS_PSSM: a novel predictor for liquid\u2013liquid protein separation identification based on evolutionary information and a deep neural network","display_name":"PredLLPS_PSSM: a novel predictor for liquid\u2013liquid protein separation identification based on evolutionary information and a deep neural network","publication_year":2023,"publication_date":"2023-08-22","ids":{"openalex":"https://openalex.org/W4386083644","doi":"https://doi.org/10.1093/bib/bbad299","pmid":"https://pubmed.ncbi.nlm.nih.gov/37609923"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad299","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad299","pdf_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad299/51711270/bbad299.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad299/51711270/bbad299.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088314609","display_name":"Shengming Zhou","orcid":"https://orcid.org/0000-0003-1809-4415"},"institutions":[{"id":"https://openalex.org/I43313876","display_name":"Dalian Maritime University","ror":"https://ror.org/002b7nr53","country_code":"CN","type":"education","lineage":["https://openalex.org/I43313876"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shengming Zhou","raw_affiliation_strings":["School of Science, Dalian Maritime University , Dalian 116026 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science, Dalian Maritime University , Dalian 116026 , China","institution_ids":["https://openalex.org/I43313876"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112985522","display_name":"Yetong Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I43313876","display_name":"Dalian Maritime University","ror":"https://ror.org/002b7nr53","country_code":"CN","type":"education","lineage":["https://openalex.org/I43313876"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yetong Zhou","raw_affiliation_strings":["School of Science, Dalian Maritime University , Dalian 116026 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science, Dalian Maritime University , Dalian 116026 , China","institution_ids":["https://openalex.org/I43313876"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100365643","display_name":"Tian Liu","orcid":"https://orcid.org/0000-0001-9768-5496"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]},{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tian Liu","raw_affiliation_strings":["School of Bioengineering, Dalian University of Technology , Dalian 116024 , China"],"raw_orcid":"https://orcid.org/0000-0001-9768-5496","affiliations":[{"raw_affiliation_string":"School of Bioengineering, Dalian University of Technology , Dalian 116024 , China","institution_ids":["https://openalex.org/I27357992","https://openalex.org/I4210092944"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102829347","display_name":"Jia Zheng","orcid":"https://orcid.org/0000-0002-5757-7113"},"institutions":[{"id":"https://openalex.org/I43313876","display_name":"Dalian Maritime University","ror":"https://ror.org/002b7nr53","country_code":"CN","type":"education","lineage":["https://openalex.org/I43313876"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jia Zheng","raw_affiliation_strings":["School of Science, Dalian Maritime University , Dalian 116026 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science, Dalian Maritime University , Dalian 116026 , China","institution_ids":["https://openalex.org/I43313876"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066126756","display_name":"Cangzhi Jia","orcid":"https://orcid.org/0000-0002-4682-2881"},"institutions":[{"id":"https://openalex.org/I43313876","display_name":"Dalian Maritime University","ror":"https://ror.org/002b7nr53","country_code":"CN","type":"education","lineage":["https://openalex.org/I43313876"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Cangzhi Jia","raw_affiliation_strings":["School of Science, Dalian Maritime University , Dalian 116026 , China"],"raw_orcid":"https://orcid.org/0000-0002-4682-2881","affiliations":[{"raw_affiliation_string":"School of Science, Dalian Maritime University , Dalian 116026 , China","institution_ids":["https://openalex.org/I43313876"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5066126756","https://openalex.org/A5100365643","https://openalex.org/A5102829347"],"corresponding_institution_ids":["https://openalex.org/I27357992","https://openalex.org/I4210092944","https://openalex.org/I43313876"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.4373,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.90148604,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"24","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9836000204086304,"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":0.9836000204086304,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9682999849319458,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9679999947547913,"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/identification","display_name":"Identification (biology)","score":0.6450684070587158},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.6349209547042847},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5764511823654175},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.558303952217102},{"id":"https://openalex.org/keywords/separation","display_name":"Separation (statistics)","score":0.4735768735408783},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3785642981529236},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33352166414260864},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2198161780834198},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1898428499698639}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6450684070587158},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.6349209547042847},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5764511823654175},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.558303952217102},{"id":"https://openalex.org/C2776061190","wikidata":"https://www.wikidata.org/wiki/Q7451805","display_name":"Separation (statistics)","level":2,"score":0.4735768735408783},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3785642981529236},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33352166414260864},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2198161780834198},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1898428499698639},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad299","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad299","pdf_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad299/51711270/bbad299.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37609923","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37609923","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad299","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad299","pdf_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad299/51711270/bbad299.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2457750594","display_name":null,"funder_award_id":"31871959","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5457985118","display_name":"\u6606\u866bRNA\u5e72\u6270\u7684dsRNA\u5206\u5b50\u8bbe\u8ba1\u53ca\u4ee3\u8c22\u52a8\u529b\u5b66\u7814\u7a76","funder_award_id":"62071079","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7800442048","display_name":null,"funder_award_id":"32170502","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/F4320321933","display_name":"Hainan Normal University","ror":"https://ror.org/031dhcv14"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386083644.pdf"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1538131130","https://openalex.org/W1591801644","https://openalex.org/W2005572147","https://openalex.org/W2052892694","https://openalex.org/W2076063813","https://openalex.org/W2085978470","https://openalex.org/W2087322782","https://openalex.org/W2097606916","https://openalex.org/W2115434912","https://openalex.org/W2139995722","https://openalex.org/W2147580225","https://openalex.org/W2156465034","https://openalex.org/W2295598076","https://openalex.org/W2425405879","https://openalex.org/W2612935389","https://openalex.org/W2786469974","https://openalex.org/W2791848964","https://openalex.org/W2907872701","https://openalex.org/W2911964244","https://openalex.org/W2971594646","https://openalex.org/W2977849281","https://openalex.org/W2980646921","https://openalex.org/W3039241573","https://openalex.org/W3083303726","https://openalex.org/W3112123143","https://openalex.org/W3127087732","https://openalex.org/W3130281988","https://openalex.org/W3143253488","https://openalex.org/W3195165594","https://openalex.org/W4205392984","https://openalex.org/W4239510810","https://openalex.org/W4250054536","https://openalex.org/W4280540965","https://openalex.org/W4281613736","https://openalex.org/W4296779471","https://openalex.org/W6769312517","https://openalex.org/W6838194286"],"related_works":["https://openalex.org/W2071676784","https://openalex.org/W4292513318","https://openalex.org/W4308092240","https://openalex.org/W2287611352","https://openalex.org/W320684304","https://openalex.org/W1509352139","https://openalex.org/W4385464961","https://openalex.org/W2060903012","https://openalex.org/W2021161555","https://openalex.org/W4400836012"],"abstract_inverted_index":{"The":[0],"formation":[1],"of":[2,18,43,49,92,107,114,150,175],"biomolecular":[3],"condensates":[4],"by":[5],"liquid-liquid":[6],"phase":[7],"separation":[8],"(LLPS)":[9],"has":[10,24],"become":[11],"a":[12,68],"universal":[13],"mechanism":[14],"for":[15,58,73],"spatiotemporal":[16],"coordination":[17],"biological":[19],"activities":[20],"in":[21,36,173],"cells":[22],"and":[23,46,62,86,98,120,127,140,186],"been":[25],"widely":[26],"observed":[27],"to":[28,190,198],"directly":[29],"regulate":[30],"the":[31,41,47,90,100,104,112,115,148,176,180,192],"key":[32],"cellular":[33],"processes":[34],"involved":[35],"cancer":[37],"cell":[38],"pathology.":[39],"However,":[40],"complexity":[42],"protein":[44,60,75],"sequences":[45],"diversity":[48],"conformations":[50],"are":[51],"inherently":[52],"disordered,":[53],"which":[54],"poses":[55],"great":[56],"challenges":[57],"LLPS":[59,74,101,164],"calculations":[61],"experimental":[63],"research.":[64],"Herein,":[65],"we":[66,95,157],"proposed":[67],"novel":[69],"predictor":[70],"named":[71],"PredLLPS_PSSM":[72,123,151,159],"identification":[76],"based":[77],"only":[78],"on":[79,160],"sequence":[80],"evolution":[81],"information.":[82],"Because":[83],"finding":[84],"real":[85],"reliable":[87],"samples":[88],"is":[89],"cornerstone":[91],"building":[93],"predictors,":[94],"collected":[96],"anew":[97],"collated":[99],"proteins":[102,165],"from":[103,166],"latest":[105],"versions":[106],"three":[108,135,167],"databases.":[109,177],"By":[110],"comparing":[111],"performance":[113],"position-specific":[116],"score":[117],"matrix":[118],"(PSSM)":[119],"word":[121],"embedding,":[122],"combined":[124],"PSSM-based":[125],"information":[126],"two":[128,141],"deep":[129],"learning":[130],"frameworks.":[131],"Independent":[132],"tests":[133],"using":[134],"existing":[136],"independent":[137,144],"test":[138,145],"datasets":[139,146],"newly":[142],"constructed":[143],"demonstrated":[147],"superiority":[149],"compared":[152],"with":[153],"state-of-the-art":[154],"methods.":[155],"Furthermore,":[156],"tested":[158],"nine":[161],"experimentally":[162],"identified":[163],"insects":[168],"that":[169],"were":[170,188],"not":[171],"included":[172],"any":[174],"In":[178],"addition,":[179],"powerful":[181],"Shapley":[182],"Additive":[183],"exPlanation":[184],"algorithm":[185],"heatmap":[187],"applied":[189],"find":[191],"most":[193],"critical":[194],"amino":[195],"acids":[196],"relevant":[197],"LLPS.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
