{"id":"https://openalex.org/W4413798564","doi":"https://doi.org/10.1186/s13321-025-01083-4","title":"Systematic benchmarking of 13 AI methods for predicting cyclic peptide membrane permeability","display_name":"Systematic benchmarking of 13 AI methods for predicting cyclic peptide membrane permeability","publication_year":2025,"publication_date":"2025-08-28","ids":{"openalex":"https://openalex.org/W4413798564","doi":"https://doi.org/10.1186/s13321-025-01083-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/40877984"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01083-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01083-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01083-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01083-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100431754","display_name":"Wei Liu","orcid":"https://orcid.org/0000-0002-1916-4684"},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Wei Liu","raw_affiliation_strings":["Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street, Singapore, 138671, Singapore. liuwei@bii.a-star.edu.sg","Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street,  Singapore, 138671, Singapore"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street, Singapore, 138671, Singapore. liuwei@bii.a-star.edu.sg","institution_ids":[]},{"raw_affiliation_string":"Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street,  Singapore, 138671, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100368371","display_name":"Jianguo Li","orcid":"https://orcid.org/0000-0002-5544-6451"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Jianguo Li","raw_affiliation_strings":["Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street, Singapore, 138671, Singapore","Singapore Eye Research Institute, 20 College Rd, Singapore, 169856, Singapore","Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street,  Singapore, 138671, Singapore"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street, Singapore, 138671, Singapore","institution_ids":[]},{"raw_affiliation_string":"Singapore Eye Research Institute, 20 College Rd, Singapore, 169856, Singapore","institution_ids":[]},{"raw_affiliation_string":"Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street,  Singapore, 138671, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045760818","display_name":"Chandra Verma","orcid":"https://orcid.org/0000-0003-0733-9798"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Chandra S. Verma","raw_affiliation_strings":["Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street, Singapore, 138671, Singapore","Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore","School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore , 637551, Singapore","Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street,  Singapore, 138671, Singapore"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street, Singapore, 138671, Singapore","institution_ids":[]},{"raw_affiliation_string":"Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore , 637551, Singapore","institution_ids":[]},{"raw_affiliation_string":"Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street,  Singapore, 138671, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032667101","display_name":"Hwee Kuan Lee","orcid":"https://orcid.org/0000-0003-1932-5377"},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Hwee Kuan Lee","raw_affiliation_strings":["Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street, Singapore, 138671, Singapore. leehk@bii.a-star.edu.sg","Centre for Frontier AI Research, Agency for Science, Technology and Research, 1 Fusionopolis Way, Singapore, 138671, Singapore. leehk@bii.a-star.edu.sg","International Research Laboratory on Artificial Intelligence, Agency for Science, Technology and Research, 1 Fusionopolis Way, Singapore, 138671, Singapore. leehk@bii.a-star.edu.sg","School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore , 637551, Singapore. leehk@bii.a-star.edu.sg","School of Computing, National University of Singapore, 13 Computing Drive, Singapore, 117417, Singapore. leehk@bii.a-star.edu.sg","Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street,  Singapore, 138671, Singapore","School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore\n, 637551, Singapore"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street, Singapore, 138671, Singapore. leehk@bii.a-star.edu.sg","institution_ids":[]},{"raw_affiliation_string":"Centre for Frontier AI Research, Agency for Science, Technology and Research, 1 Fusionopolis Way, Singapore, 138671, Singapore. leehk@bii.a-star.edu.sg","institution_ids":[]},{"raw_affiliation_string":"International Research Laboratory on Artificial Intelligence, Agency for Science, Technology and Research, 1 Fusionopolis Way, Singapore, 138671, Singapore. leehk@bii.a-star.edu.sg","institution_ids":[]},{"raw_affiliation_string":"School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore , 637551, Singapore. leehk@bii.a-star.edu.sg","institution_ids":[]},{"raw_affiliation_string":"School of Computing, National University of Singapore, 13 Computing Drive, Singapore, 117417, Singapore. leehk@bii.a-star.edu.sg","institution_ids":[]},{"raw_affiliation_string":"Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopilis Street,  Singapore, 138671, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]},{"raw_affiliation_string":"School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore\n, 637551, Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100431754"],"corresponding_institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":1.7145,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.85877538,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"17","issue":"1","first_page":"129","last_page":"129"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9983999729156494,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9980000257492065,"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/benchmarking","display_name":"Benchmarking","score":0.7149159908294678},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5655215978622437},{"id":"https://openalex.org/keywords/cyclic-peptide","display_name":"Cyclic peptide","score":0.5192575454711914},{"id":"https://openalex.org/keywords/permeability","display_name":"Permeability (electromagnetism)","score":0.41992902755737305},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3835132420063019},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.38306981325149536},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.360340416431427},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.35536932945251465},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.35333406925201416},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13782966136932373},{"id":"https://openalex.org/keywords/business","display_name":"Business","score":0.08636593818664551}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7149159908294678},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5655215978622437},{"id":"https://openalex.org/C60984968","wikidata":"https://www.wikidata.org/wiki/Q389172","display_name":"Cyclic peptide","level":3,"score":0.5192575454711914},{"id":"https://openalex.org/C120882062","wikidata":"https://www.wikidata.org/wiki/Q28352","display_name":"Permeability (electromagnetism)","level":3,"score":0.41992902755737305},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3835132420063019},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.38306981325149536},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.360340416431427},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.35536932945251465},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.35333406925201416},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13782966136932373},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.08636593818664551},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13321-025-01083-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01083-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01083-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:40877984","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40877984","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:2209c97b2a25427884a626a428a7fd55","is_oa":true,"landing_page_url":"https://doaj.org/article/2209c97b2a25427884a626a428a7fd55","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-12 (2025)","raw_type":"article"},{"id":"pmh:oai:dr.ntu.edu.sg:10356/209328","is_oa":false,"landing_page_url":"https://hdl.handle.net/10356/209328","pdf_url":null,"source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12392647","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12392647","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01083-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01083-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01083-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320696","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09"},{"id":"https://openalex.org/F4320331617","display_name":"National Supercomputing Centre Singapore","ror":null},{"id":"https://openalex.org/F4320335846","display_name":"Biomedical Research Council","ror":"https://ror.org/03xy0wx88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413798564.pdf","grobid_xml":"https://content.openalex.org/works/W4413798564.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1904678284","https://openalex.org/W1988137261","https://openalex.org/W1988315803","https://openalex.org/W2004926660","https://openalex.org/W2033495141","https://openalex.org/W2045093121","https://openalex.org/W2064675550","https://openalex.org/W2065889205","https://openalex.org/W2066273100","https://openalex.org/W2076498053","https://openalex.org/W2110485445","https://openalex.org/W2115412287","https://openalex.org/W2119821739","https://openalex.org/W2186110136","https://openalex.org/W2275988317","https://openalex.org/W2406943157","https://openalex.org/W2529268217","https://openalex.org/W2594183968","https://openalex.org/W2785477444","https://openalex.org/W2794209590","https://openalex.org/W2895931706","https://openalex.org/W2911964244","https://openalex.org/W2912930263","https://openalex.org/W2945543430","https://openalex.org/W2966357564","https://openalex.org/W2968734407","https://openalex.org/W2968953851","https://openalex.org/W3082499071","https://openalex.org/W3104896896","https://openalex.org/W3127297964","https://openalex.org/W3177545261","https://openalex.org/W3207696368","https://openalex.org/W4206627645","https://openalex.org/W4220811801","https://openalex.org/W4232529163","https://openalex.org/W4293461777","https://openalex.org/W4309218736","https://openalex.org/W4327694659","https://openalex.org/W4327698599","https://openalex.org/W4388798297","https://openalex.org/W4391231361","https://openalex.org/W4401103154","https://openalex.org/W4403833137","https://openalex.org/W4409643576","https://openalex.org/W4410077805"],"related_works":["https://openalex.org/W4406161738","https://openalex.org/W2589939877","https://openalex.org/W2081553665","https://openalex.org/W2892113376","https://openalex.org/W2030585732","https://openalex.org/W3012180934","https://openalex.org/W2078683866","https://openalex.org/W2063421454","https://openalex.org/W2088029223","https://openalex.org/W3209239669"],"abstract_inverted_index":{"Cyclic":[0],"peptides":[1],"are":[2,156],"promising":[3],"drug":[4],"candidates":[5],"due":[6],"to":[7,10,19,76,158,203,214],"their":[8,23],"ability":[9],"modulate":[11],"intracellular":[12],"protein-protein":[13],"interactions,":[14],"a":[15,89],"property":[16],"often":[17],"inaccessible":[18],"small":[20],"molecules.":[21],"However,":[22],"typically":[24],"poor":[25],"membrane":[26,101],"permeability":[27,35,64,124],"limits":[28],"therapeutic":[29],"applicability.":[30],"Accurate":[31],"computational":[32],"prediction":[33,65,140,218],"of":[34,40,71,92,108,162,227],"can":[36],"accelerate":[37],"the":[38,127,160,182,224],"identification":[39],"cell-permeable":[41],"candidates,":[42],"reducing":[43],"reliance":[44],"on":[45,173],"time-consuming":[46],"and":[47,80,116,135,145,153,176],"costly":[48],"experimental":[49,221],"screening.":[50],"Although":[51],"deep":[52],"learning":[53,95],"has":[54],"shown":[55],"potential":[56],"in":[57,63],"predicting":[58,98],"molecular":[59,109,114,174],"properties,":[60],"its":[61],"application":[62],"remains":[66],"underexplored.":[67],"A":[68],"systematic":[69],"evaluation":[70],"these":[72],"models":[73,96,104,229],"is":[74],"important":[75],"assess":[77,159,206],"current":[78,228],"capabilities":[79],"guide":[81],"future":[82],"development.":[83],"In":[84],"this":[85],"study,":[86],"we":[87],"conduct":[88],"comprehensive":[90],"benchmark":[91],"13":[93],"machine":[94],"for":[97,234],"cyclic":[99,133],"peptide":[100],"permeability.":[102],"These":[103],"cover":[105],"four":[106],"types":[107],"representations:":[110],"fingerprints,":[111],"SMILES":[112],"strings,":[113],"graphs,":[115],"2D":[117],"images.":[118],"We":[119],"use":[120],"experimentally":[121],"measured":[122],"PAMPA":[123],"data":[125],"from":[126],"CycPeptMPDB":[128],"database,":[129],"comprising":[130],"nearly":[131],"6000":[132],"peptides,":[134],"evaluate":[136],"performance":[137,170,192],"across":[138,193],"three":[139],"tasks:":[141],"regression,":[142],"binary":[143],"classification,":[144],"soft-label":[146],"classification.":[147,198],"Two":[148],"data-splitting":[149],"strategies,":[150],"random":[151,215],"split":[152],"scaffold":[154],"split,":[155],"used":[157],"generalizability":[161,212],"trained":[163],"models.":[164],"Our":[165],"results":[166],"show":[167],"that":[168],"model":[169,177,211],"depends":[171],"strongly":[172],"representation":[175],"architecture.":[178],"Graph-based":[179],"models,":[180],"particularly":[181],"Directed":[183],"Message":[184],"Passing":[185],"Neural":[186],"Network":[187],"(DMPNN),":[188],"consistently":[189],"achieve":[190],"top":[191],"tasks.":[194],"Regression":[195],"generally":[196],"outperforms":[197],"Scaffold-based":[199],"splitting,":[200],"although":[201],"intended":[202],"more":[204],"rigorously":[205],"generalization,":[207],"yields":[208],"substantially":[209],"lower":[210],"compared":[213],"splitting.":[216],"Comparing":[217],"errors":[219],"with":[220],"variability":[222],"highlights":[223],"practical":[225],"value":[226],"while":[230],"also":[231],"indicating":[232],"room":[233],"further":[235],"improvement.":[236]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}