{"id":"https://openalex.org/W4415293334","doi":"https://doi.org/10.1371/journal.pcbi.1013590","title":"Memorization bias impacts modeling of alternative conformational states of solute carrier membrane proteins with methods from deep learning","display_name":"Memorization bias impacts modeling of alternative conformational states of solute carrier membrane proteins with methods from deep learning","publication_year":2025,"publication_date":"2025-10-17","ids":{"openalex":"https://openalex.org/W4415293334","doi":"https://doi.org/10.1371/journal.pcbi.1013590","pmid":"https://pubmed.ncbi.nlm.nih.gov/41105726"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013590","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013590","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013590","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020409015","display_name":"G.V.T. Swapna","orcid":"https://orcid.org/0000-0001-9342-2525"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I165799507","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94","country_code":"US","type":"education","lineage":["https://openalex.org/I165799507"]},{"id":"https://openalex.org/I2802203029","display_name":"Johnson University","ror":"https://ror.org/04dpnfr42","country_code":"US","type":"education","lineage":["https://openalex.org/I2802203029"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"G.V.T. Swapna","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, United States of America","Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway New Jersey, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, United States of America","institution_ids":["https://openalex.org/I165799507"]},{"raw_affiliation_string":"Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway New Jersey, United States of America","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I2802203029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053706251","display_name":"Namita Dube","orcid":"https://orcid.org/0000-0002-2107-4899"},"institutions":[{"id":"https://openalex.org/I165799507","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94","country_code":"US","type":"education","lineage":["https://openalex.org/I165799507"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Namita Dube","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, United States of America","institution_ids":["https://openalex.org/I165799507"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077373617","display_name":"Monica J. Roth","orcid":"https://orcid.org/0000-0002-2219-0402"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I2802203029","display_name":"Johnson University","ror":"https://ror.org/04dpnfr42","country_code":"US","type":"education","lineage":["https://openalex.org/I2802203029"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Monica J. Roth","raw_affiliation_strings":["Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway New Jersey, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway New Jersey, United States of America","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I2802203029"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091026686","display_name":"G.T. Montelione","orcid":"https://orcid.org/0000-0002-9440-3059"},"institutions":[{"id":"https://openalex.org/I165799507","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94","country_code":"US","type":"education","lineage":["https://openalex.org/I165799507"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gaetano T. Montelione","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-9440-3059","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York, United States of America","institution_ids":["https://openalex.org/I165799507"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5020409015","https://openalex.org/A5053706251","https://openalex.org/A5077373617","https://openalex.org/A5091026686"],"corresponding_institution_ids":["https://openalex.org/I102322142","https://openalex.org/I165799507","https://openalex.org/I2802203029"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.3365,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.82920759,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"21","issue":"10","first_page":"e1013590","last_page":"e1013590"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991000294685364,"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":0.9991000294685364,"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/T10112","display_name":"HIV Research and Treatment","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9980000257492065,"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/membrane-protein","display_name":"Membrane protein","score":0.5205000042915344},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.511900007724762},{"id":"https://openalex.org/keywords/integral-membrane-protein","display_name":"Integral membrane protein","score":0.4422000050544739},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4406999945640564},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.42419999837875366},{"id":"https://openalex.org/keywords/conformational-change","display_name":"Conformational change","score":0.38089999556541443},{"id":"https://openalex.org/keywords/membrane-transport-protein","display_name":"Membrane transport protein","score":0.3797000050544739},{"id":"https://openalex.org/keywords/structural-biology","display_name":"Structural biology","score":0.37290000915527344},{"id":"https://openalex.org/keywords/transport-protein","display_name":"Transport protein","score":0.3443000018596649},{"id":"https://openalex.org/keywords/protein-engineering","display_name":"Protein engineering","score":0.3440000116825104}],"concepts":[{"id":"https://openalex.org/C144647389","wikidata":"https://www.wikidata.org/wiki/Q423042","display_name":"Membrane protein","level":3,"score":0.5205000042915344},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.511900007724762},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.5077999830245972},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4487999975681305},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44760000705718994},{"id":"https://openalex.org/C161200384","wikidata":"https://www.wikidata.org/wiki/Q1757382","display_name":"Integral membrane protein","level":4,"score":0.4422000050544739},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4406999945640564},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.42419999837875366},{"id":"https://openalex.org/C2777339483","wikidata":"https://www.wikidata.org/wiki/Q647203","display_name":"Conformational change","level":2,"score":0.38089999556541443},{"id":"https://openalex.org/C115335371","wikidata":"https://www.wikidata.org/wiki/Q142943","display_name":"Membrane transport protein","level":4,"score":0.3797000050544739},{"id":"https://openalex.org/C191120209","wikidata":"https://www.wikidata.org/wiki/Q908902","display_name":"Structural biology","level":2,"score":0.37290000915527344},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.37070000171661377},{"id":"https://openalex.org/C57581600","wikidata":"https://www.wikidata.org/wiki/Q2449730","display_name":"Transport protein","level":2,"score":0.3443000018596649},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.3440000116825104},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.3343999981880188},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.32589998841285706},{"id":"https://openalex.org/C2778815515","wikidata":"https://www.wikidata.org/wiki/Q3408242","display_name":"Intrinsically disordered proteins","level":2,"score":0.31520000100135803},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31200000643730164},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.3084000051021576},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.2939999997615814},{"id":"https://openalex.org/C196347352","wikidata":"https://www.wikidata.org/wiki/Q24771787","display_name":"SH3 domain","level":4,"score":0.2915000021457672},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.28999999165534973},{"id":"https://openalex.org/C103038307","wikidata":"https://www.wikidata.org/wiki/Q6556360","display_name":"Lipid bilayer fusion","level":3,"score":0.2879999876022339},{"id":"https://openalex.org/C57947595","wikidata":"https://www.wikidata.org/wiki/Q7886088","display_name":"Membrane transport","level":3,"score":0.2842999994754791},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.28209999203681946},{"id":"https://openalex.org/C178910836","wikidata":"https://www.wikidata.org/wiki/Q2196961","display_name":"Molecular model","level":2,"score":0.2815000116825104},{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.27889999747276306},{"id":"https://openalex.org/C168240541","wikidata":"https://www.wikidata.org/wiki/Q45948","display_name":"Organelle","level":2,"score":0.2775000035762787},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.27720001339912415},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.275299996137619},{"id":"https://openalex.org/C96305047","wikidata":"https://www.wikidata.org/wiki/Q367473","display_name":"F\u00f6rster resonance energy transfer","level":3,"score":0.2648000121116638},{"id":"https://openalex.org/C2909404852","wikidata":"https://www.wikidata.org/wiki/Q994215","display_name":"Viral membrane","level":4,"score":0.26249998807907104},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.25450000166893005},{"id":"https://openalex.org/C179303850","wikidata":"https://www.wikidata.org/wiki/Q4300362","display_name":"Molecular recognition","level":3,"score":0.2533999979496002}],"mesh":[{"descriptor_ui":"D000070590","descriptor_name":"Solute Carrier Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000070590","descriptor_name":"Solute Carrier Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000070590","descriptor_name":"Solute Carrier Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000070590","descriptor_name":"Solute Carrier Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000070590","descriptor_name":"Solute Carrier Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000070590","descriptor_name":"Solute Carrier Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1013590","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013590","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:41105726","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41105726","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:8dbca5ca4a014d0aa1db1c8b8813678c","is_oa":true,"landing_page_url":"https://doaj.org/article/8dbca5ca4a014d0aa1db1c8b8813678c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 10, p e1013590 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11359550","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12551959","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013590","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013590","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3846999418","display_name":null,"funder_award_id":"GM122518","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5362398012","display_name":null,"funder_award_id":"R35 GM141818","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320309500","display_name":"Rensselaer Polytechnic Institute","ror":"https://ror.org/01rtyzb94"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":70,"referenced_works":["https://openalex.org/W1951660422","https://openalex.org/W1965402353","https://openalex.org/W1970375875","https://openalex.org/W2051545676","https://openalex.org/W2058447887","https://openalex.org/W2065283382","https://openalex.org/W2069458148","https://openalex.org/W2075560763","https://openalex.org/W2083153125","https://openalex.org/W2085008263","https://openalex.org/W2085036090","https://openalex.org/W2109523366","https://openalex.org/W2110897805","https://openalex.org/W2113336835","https://openalex.org/W2121688928","https://openalex.org/W2126289782","https://openalex.org/W2141366228","https://openalex.org/W2146640609","https://openalex.org/W2303521084","https://openalex.org/W2326139126","https://openalex.org/W2425595198","https://openalex.org/W2600704321","https://openalex.org/W2768448654","https://openalex.org/W2797346936","https://openalex.org/W2804822363","https://openalex.org/W2905846362","https://openalex.org/W2921827279","https://openalex.org/W2946114466","https://openalex.org/W2951041301","https://openalex.org/W2990430418","https://openalex.org/W3045541940","https://openalex.org/W3078821236","https://openalex.org/W3111189917","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3198923619","https://openalex.org/W3199246256","https://openalex.org/W3210360742","https://openalex.org/W4211196614","https://openalex.org/W4214847177","https://openalex.org/W4225552973","https://openalex.org/W4229000770","https://openalex.org/W4281790889","https://openalex.org/W4292636432","https://openalex.org/W4297235560","https://openalex.org/W4310159409","https://openalex.org/W4321090885","https://openalex.org/W4327550249","https://openalex.org/W4377089153","https://openalex.org/W4382601731","https://openalex.org/W4385236300","https://openalex.org/W4385620526","https://openalex.org/W4386469263","https://openalex.org/W4386793933","https://openalex.org/W4387300387","https://openalex.org/W4388302761","https://openalex.org/W4388627063","https://openalex.org/W4388924564","https://openalex.org/W4391887943","https://openalex.org/W4393559298","https://openalex.org/W4396721167","https://openalex.org/W4396895148","https://openalex.org/W4399276094","https://openalex.org/W4401844424","https://openalex.org/W4401895022","https://openalex.org/W4402722647","https://openalex.org/W4404568702","https://openalex.org/W4406063185","https://openalex.org/W4407720093","https://openalex.org/W4412165572"],"related_works":[],"abstract_inverted_index":{"The":[0],"Solute":[1],"Carrier":[2],"(SLC)":[3],"superfamily":[4],"of":[5,13,61,82,87,99,112,114,130,138,168,179,226,242],"integral":[6,234],"membrane":[7,235],"proteins":[8,52,100,143,229],"transport":[9,39],"a":[10,148,156,243],"wide":[11],"array":[12],"small":[14],"molecules":[15],"across":[16],"plasma":[17],"and":[18,21,27,45,64,119,127,146,219],"organelle":[19],"membranes,":[20],"function":[22],"as":[23,28],"important":[24],"drug":[25],"transporters":[26],"viral":[29,251],"receptors.":[30],"They":[31],"populate":[32],"different":[33],"conformational":[34,47,85,97,117,177,210,224],"states":[35,86,98,178,211],"during":[36],"the":[37,115,125,136,165,175,186,208,214,240],"solute":[38],"process,":[40,153],"including":[41,238],"outward-open,":[42],"intermediate":[43],"(occluded),":[44],"inward-open":[46],"states.":[48],"For":[49],"some":[50],"SLC":[51,88,131,142,170,180,228],"this":[53],"structural":[54],"\"flipping\"":[55],"corresponds":[56],"to":[57,172],"swapping":[58],"between":[59],"conformations":[60,129],"their":[62],"N-terminal":[63],"C-terminal":[65],"symmetry-related":[66],"sub-structures.":[67],"Conventional":[68],"AlphaFold2,":[69],"AlphaFold3,":[70],"or":[71],"Evolutionary":[72],"Scale":[73],"Modeling":[74],"methods":[75,106],"typically":[76],"generate":[77],"models":[78,189],"for":[79,94,222,232,250],"only":[80],"one":[81,113],"these":[83,105],"multiple":[84,96],"proteins.":[89,132,181],"While":[90],"several":[91,233],"AI-based":[92],"protocols":[93],"modeling":[95,141,160,223],"have":[101],"been":[102],"described":[103,158],"recently,":[104],"are":[107],"often":[108],"impacted":[109],"by":[110,193,213],"\"memorization\"":[111],"alternative":[116],"states,":[118],"do":[120],"not":[121],"always":[122],"provide":[123],"both":[124],"inward-":[126],"outward-open":[128],"Here":[133],"we":[134],"assess":[135],"impact":[137],"memorization":[139],"in":[140,207],"with":[144,195],"AlphaFold2/3,":[145],"describe":[147],"combined":[149],"ESM":[150],"-":[151],"template-based-modeling":[152],"based":[154],"on":[155,164],"previously":[157],"template-based":[159],"method":[161],"that":[162,201],"relies":[163],"internal":[166],"pseudo-symmetry":[167],"many":[169],"proteins,":[171],"consistently":[173],"model":[174],"alternate":[176],"We":[182],"also":[183],"demonstrate":[184],"how":[185],"resulting":[187],"multi-state":[188],"can":[190],"be":[191],"validated":[192],"comparison":[194],"sequence-based":[196],"evolutionary":[197],"co-variance":[198],"data":[199],"(ECs)":[200],"encode":[202],"information":[203],"about":[204],"contacts":[205],"present":[206],"various":[209],"adopted":[212],"protein.":[215],"This":[216],"simple,":[217],"rapid,":[218],"robust":[220],"approach":[221],"landscapes":[225],"pseudo-symmetric":[227],"is":[230],"demonstrated":[231],"protein":[236,248],"transporters,":[237],"SLC35F2":[239],"receptor":[241],"feline":[244],"leukemia":[245],"virus":[246],"envelope":[247],"required":[249],"entry":[252],"into":[253],"eukaryotic":[254],"cells.":[255]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-09T13:55:54.758798","created_date":"2025-10-18T00:00:00"}
