{"id":"https://openalex.org/W7225254443","doi":"https://doi.org/10.1039/d6ra07903b","title":"When does a funnel become a trap? A G\u00f6mb\u00f6c-inspired model of protein folding landscapes","display_name":"When does a funnel become a trap? A G\u00f6mb\u00f6c-inspired model of protein folding landscapes","publication_year":2026,"publication_date":"2026-01-01","ids":{"openalex":"https://openalex.org/W7225254443","doi":"https://doi.org/10.1039/d6ra07903b","pmid":"https://pubmed.ncbi.nlm.nih.gov/42985218","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13733664"},"language":"en","primary_location":{"id":"doi:10.1039/d6ra07903b","doi":"https://doi.org/10.1039/d6ra07903b","is_oa":true,"landing_page_url":"https://doi.org/10.1039/d6ra07903b","pdf_url":"https://pubs.rsc.org/ra/article-pdf/doi/10.1039/d6ra07903b/15033433/d6ra07903b.pdf","source":{"id":"https://openalex.org/S2481244646","display_name":"RSC Advances","issn_l":"2046-2069","issn":["2046-2069"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320556","host_organization_name":"Royal Society of Chemistry","host_organization_lineage":["https://openalex.org/P4310320556"],"host_organization_lineage_names":["Royal Society of Chemistry"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"RSC Advances","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://pubs.rsc.org/ra/article-pdf/doi/10.1039/d6ra07903b/15033433/d6ra07903b.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021179531","display_name":"Sergey Shityakov","orcid":"https://orcid.org/0000-0002-6953-9771","observed_orcids":["https://orcid.org/0000-0002-6953-9771"]},"institutions":[{"id":"https://openalex.org/I173089394","display_name":"ITMO University","ror":"https://ror.org/04txgxn49","country_code":"RU","type":"education","lineage":["https://openalex.org/I173089394"]},{"id":"https://openalex.org/I17877952","display_name":"Sechenov University","ror":"https://ror.org/02yqqv993","country_code":"RU","type":"education","lineage":["https://openalex.org/I17877952"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Sergey Shityakov","raw_affiliation_strings":["Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), Izmaylovskiy Boulevard 8, Moscow, 105043, Russia","Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Lomonosova Street 9, Saint Petersburg, 191002, Russia"],"raw_orcid":"https://orcid.org/0000-0002-6953-9771","affiliations":[{"raw_affiliation_string":"Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), Izmaylovskiy Boulevard 8, Moscow, 105043, Russia","institution_ids":["https://openalex.org/I17877952"]},{"raw_affiliation_string":"Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Lomonosova Street 9, Saint Petersburg, 191002, Russia","institution_ids":["https://openalex.org/I173089394"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044909206","display_name":"\u0415\u043a\u0430\u0442\u0435\u0440\u0438\u043d\u0430 \u0412\u043b\u0430\u0434\u0438\u043c\u0438\u0440\u043e\u0432\u043d\u0430 \u0421\u043a\u043e\u0440\u0431","orcid":"https://orcid.org/0000-0003-0888-1693","observed_orcids":["https://orcid.org/0000-0003-0888-1693"]},"institutions":[{"id":"https://openalex.org/I173089394","display_name":"ITMO University","ror":"https://ror.org/04txgxn49","country_code":"RU","type":"education","lineage":["https://openalex.org/I173089394"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ekaterina V. Skorb","raw_affiliation_strings":["Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Lomonosova Street 9, Saint Petersburg, 191002, Russia"],"raw_orcid":"https://orcid.org/0000-0003-0888-1693","affiliations":[{"raw_affiliation_string":"Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Lomonosova Street 9, Saint Petersburg, 191002, Russia","institution_ids":["https://openalex.org/I173089394"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032131820","display_name":"Michael Nosonovsky","orcid":"https://orcid.org/0000-0003-0980-3670","observed_orcids":["https://orcid.org/0000-0003-0980-3670"]},"institutions":[{"id":"https://openalex.org/I173089394","display_name":"ITMO University","ror":"https://ror.org/04txgxn49","country_code":"RU","type":"education","lineage":["https://openalex.org/I173089394"]},{"id":"https://openalex.org/I17877952","display_name":"Sechenov University","ror":"https://ror.org/02yqqv993","country_code":"RU","type":"education","lineage":["https://openalex.org/I17877952"]},{"id":"https://openalex.org/I43579087","display_name":"University of Wisconsin\u2013Milwaukee","ror":"https://ror.org/031q21x57","country_code":"US","type":"education","lineage":["https://openalex.org/I43579087"]}],"countries":["RU","US"],"is_corresponding":true,"raw_author_name":"Michael Nosonovsky","raw_affiliation_strings":["College of Engineering and Applied Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA","Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), Izmaylovskiy Boulevard 8, Moscow, 105043, Russia","Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Lomonosova Street 9, Saint Petersburg, 191002, Russia"],"raw_orcid":"https://orcid.org/0000-0003-0980-3670","affiliations":[{"raw_affiliation_string":"College of Engineering and Applied Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA","institution_ids":["https://openalex.org/I43579087"]},{"raw_affiliation_string":"Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), Izmaylovskiy Boulevard 8, Moscow, 105043, Russia","institution_ids":["https://openalex.org/I17877952"]},{"raw_affiliation_string":"Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Lomonosova Street 9, Saint Petersburg, 191002, Russia","institution_ids":["https://openalex.org/I173089394"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5021179531","https://openalex.org/A5032131820"],"corresponding_institution_ids":["https://openalex.org/I173089394","https://openalex.org/I17877952","https://openalex.org/I43579087"],"apc_list":{"value":850,"currency":"GBP","value_usd":1042},"apc_paid":{"value":850,"currency":"GBP","value_usd":1042},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.72505933,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.9970999956130981,"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":0.9970999956130981,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.0010999999940395355,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-folding-landscape","display_name":"protein folding landscape","score":0.8080000281333923},{"id":"https://openalex.org/keywords/folding-funnel","display_name":"folding funnel","score":0.6060000061988831},{"id":"https://openalex.org/keywords/terrain-ruggedness","display_name":"terrain ruggedness","score":0.9290000200271606},{"id":"https://openalex.org/keywords/protein-foldability","display_name":"protein foldability","score":0.7990000247955322},{"id":"https://openalex.org/keywords/rosetta-spacecraft","display_name":"Rosetta","score":0.7559999823570251},{"id":"https://openalex.org/keywords/alphafold-3","display_name":"AlphaFold3","score":0.953000009059906}],"concepts":[{"id":"https://openalex.org/C17435862","wikidata":"https://www.wikidata.org/wiki/Q29957","display_name":"Funnel","level":2,"score":0.925599992275238},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.7057999968528748},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.6843000054359436},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.5105999708175659},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.48730000853538513},{"id":"https://openalex.org/C174507519","wikidata":"https://www.wikidata.org/wiki/Q5464306","display_name":"Folding funnel","level":5,"score":0.37279999256134033},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3711000084877014},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.33329999446868896},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3310000002384186},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3287000060081482},{"id":"https://openalex.org/C2988375501","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein stability","level":2,"score":0.3102000057697296},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3093999922275543},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.30219998955726624},{"id":"https://openalex.org/C32598905","wikidata":"https://www.wikidata.org/wiki/Q6497130","display_name":"Lattice protein","level":3,"score":0.2847000062465668},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.2720000147819519},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.2605000138282776},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25110000371932983}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1039/d6ra07903b","doi":"https://doi.org/10.1039/d6ra07903b","is_oa":true,"landing_page_url":"https://doi.org/10.1039/d6ra07903b","pdf_url":"https://pubs.rsc.org/ra/article-pdf/doi/10.1039/d6ra07903b/15033433/d6ra07903b.pdf","source":{"id":"https://openalex.org/S2481244646","display_name":"RSC Advances","issn_l":"2046-2069","issn":["2046-2069"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320556","host_organization_name":"Royal Society of Chemistry","host_organization_lineage":["https://openalex.org/P4310320556"],"host_organization_lineage_names":["Royal Society of Chemistry"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"RSC Advances","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13733664","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13733664/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13733664/pdf/RA-OLF-D6RA07903B.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"RSC Adv","raw_type":"Text"},{"id":"pmid:42985218","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42985218","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"RSC advances","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1039/d6ra07903b","doi":"https://doi.org/10.1039/d6ra07903b","is_oa":true,"landing_page_url":"https://doi.org/10.1039/d6ra07903b","pdf_url":"https://pubs.rsc.org/ra/article-pdf/doi/10.1039/d6ra07903b/15033433/d6ra07903b.pdf","source":{"id":"https://openalex.org/S2481244646","display_name":"RSC Advances","issn_l":"2046-2069","issn":["2046-2069"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","norway-1","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320556","host_organization_name":"Royal Society of Chemistry","host_organization_lineage":["https://openalex.org/P4310320556"],"host_organization_lineage_names":["Royal Society of Chemistry"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"RSC Advances","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G9000848727","display_name":null,"funder_award_id":"FSER-2026-0010","funder_id":"https://openalex.org/F4320327494","funder_display_name":"Ministry of Science and Higher Education of the Russian Federation"}],"funders":[{"id":"https://openalex.org/F4320327494","display_name":"Ministry of Science and Higher Education of the Russian Federation","ror":null},{"id":"https://openalex.org/F4320327682","display_name":"Fondation Schlumberger pour l\u2019Education et la Recherche","ror":"https://ror.org/004pwee45"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225254443.pdf","grobid_xml":"https://content.openalex.org/works/W7225254443.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1508705558","https://openalex.org/W1955276614","https://openalex.org/W1991194470","https://openalex.org/W2065864578","https://openalex.org/W2066195251","https://openalex.org/W2069448508","https://openalex.org/W2086779432","https://openalex.org/W2087245549","https://openalex.org/W2087729059","https://openalex.org/W2103111465","https://openalex.org/W2160721947","https://openalex.org/W2524536243","https://openalex.org/W2606439133","https://openalex.org/W2660691091","https://openalex.org/W2784059176","https://openalex.org/W3127370042","https://openalex.org/W4229364189","https://openalex.org/W4280508965","https://openalex.org/W4282915889","https://openalex.org/W4285097413","https://openalex.org/W4285594705","https://openalex.org/W4367844563","https://openalex.org/W4412737628","https://openalex.org/W4413537671"],"related_works":["https://openalex.org/W1638868243","https://openalex.org/W2724860773","https://openalex.org/W2790109124","https://openalex.org/W7134286353","https://openalex.org/W1977203247","https://openalex.org/W7095794287","https://openalex.org/W2945082465","https://openalex.org/W1837818860","https://openalex.org/W1631352946","https://openalex.org/W3107148387"],"abstract_inverted_index":{"Rosetta":[0],"and":[1,8,37],"AlphaFold3":[2],"reveals":[3],"native-like":[4],"coverages":[5],"of":[6,33],"77%":[7],"90%,":[9],"respectively,":[10],"showing":[11],"qualitative":[12],"correspondence":[13],"with":[14,53],"the":[15,27],"G\u00f6mb\u00f6c":[16],"model's":[17],"success":[18],"rates":[19],"at":[20],"low":[21],"ruggedness.":[22],"These":[23],"findings":[24],"suggest":[25],"that":[26],"G\u00f6mb\u00f6c-inspired":[28],"model":[29],"captures":[30],"essential":[31],"features":[32],"folding":[34],"landscape":[35],"quality":[36],"may":[38],"serve":[39],"as":[40],"a":[41],"useful":[42],"heuristic":[43],"for":[44],"comparing":[45],"foldability":[46],"across":[47],"different":[48],"systems,":[49],"bridging":[50],"mathematical":[51],"topology":[52],"protein":[54],"biophysics.":[55]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-11-05T00:00:00"}