{"id":"https://openalex.org/W7160998474","doi":"https://doi.org/10.1007/s10822-026-00831-4","title":"A systematic evaluation of protein allosteric site prediction tools with independent datasets","display_name":"A systematic evaluation of protein allosteric site prediction tools with independent datasets","publication_year":2026,"publication_date":"2026-05-13","ids":{"openalex":"https://openalex.org/W7160998474","doi":"https://doi.org/10.1007/s10822-026-00831-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/42126486"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-026-00831-4","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-026-00831-4","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","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/A5062055806","display_name":"Yuanbao Ai","orcid":"https://orcid.org/0000-0002-9008-2884"},"institutions":[{"id":"https://openalex.org/I4210150320","display_name":"Center of Hubei Cooperative Innovation for Emissions Trading System","ror":"https://ror.org/03nrzqb76","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210150320"]},{"id":"https://openalex.org/I74525822","display_name":"Hubei University of Technology","ror":"https://ror.org/02d3fj342","country_code":"CN","type":"education","lineage":["https://openalex.org/I74525822"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanbao Ai","raw_affiliation_strings":["Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, 430068, China","Key Laboratory of Fermentation Engineering (Ministry of Education), National \"111\" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, 430068, China","institution_ids":["https://openalex.org/I4210150320","https://openalex.org/I74525822"]},{"raw_affiliation_string":"Key Laboratory of Fermentation Engineering (Ministry of Education), National \"111\" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China","institution_ids":["https://openalex.org/I74525822"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065859286","display_name":"Hui Li","orcid":"https://orcid.org/0000-0001-9198-3951"},"institutions":[{"id":"https://openalex.org/I4210150320","display_name":"Center of Hubei Cooperative Innovation for Emissions Trading System","ror":"https://ror.org/03nrzqb76","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210150320"]},{"id":"https://openalex.org/I74525822","display_name":"Hubei University of Technology","ror":"https://ror.org/02d3fj342","country_code":"CN","type":"education","lineage":["https://openalex.org/I74525822"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haixiao Li","raw_affiliation_strings":["Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, 430068, China","Key Laboratory of Fermentation Engineering (Ministry of Education), National \"111\" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, 430068, China","institution_ids":["https://openalex.org/I4210150320","https://openalex.org/I74525822"]},{"raw_affiliation_string":"Key Laboratory of Fermentation Engineering (Ministry of Education), National \"111\" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China","institution_ids":["https://openalex.org/I74525822"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136049716","display_name":"Xuemei Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150320","display_name":"Center of Hubei Cooperative Innovation for Emissions Trading System","ror":"https://ror.org/03nrzqb76","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210150320"]},{"id":"https://openalex.org/I74525822","display_name":"Hubei University of Technology","ror":"https://ror.org/02d3fj342","country_code":"CN","type":"education","lineage":["https://openalex.org/I74525822"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuemei Huang","raw_affiliation_strings":["Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, 430068, China","Key Laboratory of Fermentation Engineering (Ministry of Education), National \"111\" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, 430068, China","institution_ids":["https://openalex.org/I4210150320","https://openalex.org/I74525822"]},{"raw_affiliation_string":"Key Laboratory of Fermentation Engineering (Ministry of Education), National \"111\" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China","institution_ids":["https://openalex.org/I74525822"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100358485","display_name":"Sen Liu","orcid":"https://orcid.org/0000-0001-5182-7241"},"institutions":[{"id":"https://openalex.org/I4210150320","display_name":"Center of Hubei Cooperative Innovation for Emissions Trading System","ror":"https://ror.org/03nrzqb76","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210150320"]},{"id":"https://openalex.org/I74525822","display_name":"Hubei University of Technology","ror":"https://ror.org/02d3fj342","country_code":"CN","type":"education","lineage":["https://openalex.org/I74525822"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Sen Liu","raw_affiliation_strings":["Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, 430068, China. senliu.ctgu@gmail.com","Key Laboratory of Fermentation Engineering (Ministry of Education), National \"111\" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China. senliu.ctgu@gmail.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Wuhan, 430068, China. senliu.ctgu@gmail.com","institution_ids":["https://openalex.org/I4210150320","https://openalex.org/I74525822"]},{"raw_affiliation_string":"Key Laboratory of Fermentation Engineering (Ministry of Education), National \"111\" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China. senliu.ctgu@gmail.com","institution_ids":["https://openalex.org/I74525822"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100358485"],"corresponding_institution_ids":["https://openalex.org/I4210150320","https://openalex.org/I74525822"],"apc_list":{"value":3690,"currency":"USD","value_usd":3690},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.49725817,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"40","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7688000202178955,"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":0.7688000202178955,"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":0.10090000182390213,"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":0.044599998742341995,"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/allosteric-regulation","display_name":"Allosteric regulation","score":0.9221000075340271},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.5979999899864197},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4690000116825104},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.4677000045776367},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.384799987077713},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.3538999855518341}],"concepts":[{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.9221000075340271},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.5979999899864197},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5586000084877014},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4745999872684479},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4690000116825104},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.4677000045776367},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4611999988555908},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4212000072002411},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.384799987077713},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.367000013589859},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3538999855518341},{"id":"https://openalex.org/C63882131","wikidata":"https://www.wikidata.org/wiki/Q17122954","display_name":"Strengths and weaknesses","level":2,"score":0.34860000014305115},{"id":"https://openalex.org/C109964505","wikidata":"https://www.wikidata.org/wiki/Q3321436","display_name":"Allosteric enzyme","level":4,"score":0.3131999969482422},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.30640000104904175},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.2987000048160553},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.27720001339912415},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.26159998774528503}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098437","descriptor_name":"Prediction Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098437","descriptor_name":"Prediction Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098437","descriptor_name":"Prediction Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-026-00831-4","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-026-00831-4","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:42126486","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42126486","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 computer-aided molecular design","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6522406726","display_name":null,"funder_award_id":"31971150","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":47,"referenced_works":["https://openalex.org/W2025465832","https://openalex.org/W2041205020","https://openalex.org/W2046468203","https://openalex.org/W2048934130","https://openalex.org/W2074929227","https://openalex.org/W2101017457","https://openalex.org/W2116993067","https://openalex.org/W2125299915","https://openalex.org/W2126586461","https://openalex.org/W2157605186","https://openalex.org/W2164088236","https://openalex.org/W2164897290","https://openalex.org/W2254489325","https://openalex.org/W2295598076","https://openalex.org/W2516773138","https://openalex.org/W2766298563","https://openalex.org/W2799327292","https://openalex.org/W2810768392","https://openalex.org/W2896403345","https://openalex.org/W2945661338","https://openalex.org/W2981180040","https://openalex.org/W3005865249","https://openalex.org/W3097974261","https://openalex.org/W3130442532","https://openalex.org/W3190391706","https://openalex.org/W4200375412","https://openalex.org/W4226021347","https://openalex.org/W4285009335","https://openalex.org/W4312045153","https://openalex.org/W4320341731","https://openalex.org/W4366235057","https://openalex.org/W4367174467","https://openalex.org/W4367310075","https://openalex.org/W4368373587","https://openalex.org/W4380048860","https://openalex.org/W4386002705","https://openalex.org/W4389607948","https://openalex.org/W4391147438","https://openalex.org/W4402581865","https://openalex.org/W4407560432","https://openalex.org/W4408612760","https://openalex.org/W4412477057","https://openalex.org/W4413194247","https://openalex.org/W4413958982","https://openalex.org/W4414498278","https://openalex.org/W4415479010","https://openalex.org/W7128976251"],"related_works":[],"abstract_inverted_index":null,"counts_by_year":[],"updated_date":"2026-07-25T15:57:00.446498","created_date":"2026-05-14T00:00:00"}