{"id":"https://openalex.org/W7204662235","doi":"https://doi.org/10.64898/2026.08.28.747885","title":"GNMCADS: Sampling For Protein Conformation Diversity With Gaussian Network Model Guided Condition Annealed Diffusion Sampler","display_name":"GNMCADS: Sampling For Protein Conformation Diversity With Gaussian Network Model Guided Condition Annealed Diffusion Sampler","publication_year":2026,"publication_date":"2026-08-28","ids":{"openalex":"https://openalex.org/W7204662235","doi":"https://doi.org/10.64898/2026.08.28.747885"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.28.747885","doi":"https://doi.org/10.64898/2026.08.28.747885","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.28.747885","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/28/2026.08.28.747885.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/28/2026.08.28.747885.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5148587635","display_name":"Ahmed Selim Uzum","orcid":"https://orcid.org/0009-0000-2954-1976","observed_orcids":["https://orcid.org/0009-0000-2954-1976"]},"institutions":[{"id":"https://openalex.org/I4405392","display_name":"Bo\u011fazi\u00e7i University","ror":"https://ror.org/03z9tma90","country_code":"TR","type":"education","lineage":["https://openalex.org/I4405392"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Ahmed Selim Uzum","raw_affiliation_strings":["Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkiye","Polymer Research Center, Bogazici University, Istanbul, Turkiye"],"raw_orcid":"https://orcid.org/0009-0000-2954-1976","affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkiye","institution_ids":["https://openalex.org/I4405392"]},{"raw_affiliation_string":"Polymer Research Center, Bogazici University, Istanbul, Turkiye","institution_ids":["https://openalex.org/I4405392"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038256975","display_name":"T\u00fcrkan Halilo\u01e7lu","orcid":"https://orcid.org/0000-0002-1279-5803","observed_orcids":["https://orcid.org/0000-0002-1279-5803"]},"institutions":[{"id":"https://openalex.org/I4405392","display_name":"Bo\u011fazi\u00e7i University","ror":"https://ror.org/03z9tma90","country_code":"TR","type":"education","lineage":["https://openalex.org/I4405392"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Turkan Haliloglu","raw_affiliation_strings":["Department of Chemical Engineering, Bogazici University, Istanbul, Turkiye","Polymer Research Center, Bogazici University, Istanbul, Turkiye"],"raw_orcid":"https://orcid.org/0000-0002-1279-5803","affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, Bogazici University, Istanbul, Turkiye","institution_ids":["https://openalex.org/I4405392"]},{"raw_affiliation_string":"Polymer Research Center, Bogazici University, Istanbul, Turkiye","institution_ids":["https://openalex.org/I4405392"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5148587635"],"corresponding_institution_ids":["https://openalex.org/I4405392"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"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":0.9984999895095825,"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":0.9984999895095825,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.00039999998989515007,"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":0.0003000000142492354,"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/protein-conformational-sampling","display_name":"protein conformational sampling","score":0.8859999775886536},{"id":"https://openalex.org/keywords/conformational-heterogeneity","display_name":"conformational heterogeneity","score":0.7940000295639038},{"id":"https://openalex.org/keywords/gaussian-network-model","display_name":"Gaussian network model","score":0.8700000047683716},{"id":"https://openalex.org/keywords/alphafold-3","display_name":"AlphaFold3","score":0.6039999723434448},{"id":"https://openalex.org/keywords/diffusion-models","display_name":"diffusion models","score":0.6850000023841858},{"id":"https://openalex.org/keywords/class-a-gpcrs","display_name":"class A GPCRs","score":0.8560000061988831},{"id":"https://openalex.org/keywords/membrane-transporters","display_name":"membrane transporters","score":0.8019999861717224},{"id":"https://openalex.org/keywords/protein-dynamics","display_name":"protein dynamics","score":0.6899999976158142}],"concepts":[{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.6904000043869019},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.6179999709129333},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5199999809265137},{"id":"https://openalex.org/C2775981520","wikidata":"https://www.wikidata.org/wiki/Q17156992","display_name":"Protein dynamics","level":3,"score":0.48750001192092896},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.48080000281333923},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.43790000677108765},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.41290000081062317},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.40549999475479126},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4027999937534332},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.36010000109672546},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.359499990940094},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.35760000348091125},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.3522000014781952},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3273000121116638},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.3253999948501587},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.31040000915527344},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3057999908924103},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.30489999055862427},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.3041999936103821},{"id":"https://openalex.org/C2777339483","wikidata":"https://www.wikidata.org/wiki/Q647203","display_name":"Conformational change","level":2,"score":0.30410000681877136},{"id":"https://openalex.org/C103824480","wikidata":"https://www.wikidata.org/wiki/Q185889","display_name":"Time domain","level":2,"score":0.3010999858379364},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3003999888896942},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.29919999837875366},{"id":"https://openalex.org/C74859849","wikidata":"https://www.wikidata.org/wiki/Q2466686","display_name":"Non-equilibrium thermodynamics","level":2,"score":0.28040000796318054},{"id":"https://openalex.org/C126980161","wikidata":"https://www.wikidata.org/wiki/Q863783","display_name":"Simulated annealing","level":2,"score":0.2782000005245209},{"id":"https://openalex.org/C52740198","wikidata":"https://www.wikidata.org/wiki/Q1539564","display_name":"Importance sampling","level":3,"score":0.27630001306533813},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.27549999952316284},{"id":"https://openalex.org/C2987691683","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling time","level":2,"score":0.2750999927520752},{"id":"https://openalex.org/C20326153","wikidata":"https://www.wikidata.org/wiki/Q7049638","display_name":"Nonuniform sampling","level":3,"score":0.27149999141693115},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.26899999380111694}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.08.28.747885","doi":"https://doi.org/10.64898/2026.08.28.747885","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.28.747885","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/28/2026.08.28.747885.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.08.28.747885","doi":"https://doi.org/10.64898/2026.08.28.747885","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.28.747885","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/28/2026.08.28.747885.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7204662235.pdf","grobid_xml":"https://content.openalex.org/works/W7204662235.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4417479108","https://openalex.org/W7124731324","https://openalex.org/W4402939815","https://openalex.org/W4417028074","https://openalex.org/W7203742510","https://openalex.org/W7117753534","https://openalex.org/W7118000573","https://openalex.org/W4414185028","https://openalex.org/W4393118201","https://openalex.org/W4414969529"],"abstract_inverted_index":{"Abstract":[0],"Proteins":[1],"are":[2],"dynamic":[3],"molecules":[4],"existing":[5],"in":[6,94],"diverse":[7,19,104],"conformational":[8,20,63,136],"states":[9],"underlying":[10],"their":[11],"biological":[12],"functions.":[13],"Although":[14],"recent":[15],"approaches":[16],"have":[17],"enabled":[18],"sampling":[21,64,130,137],"by":[22,74,81],"emulating":[23],"molecular":[24],"dynamics":[25],"simulations,":[26],"perturbing":[27],"evolutionary":[28],"information,":[29],"or":[30,45],"steering":[31],"internal":[32],"mechanisms":[33],"of":[34,70,86,98,103],"structure":[35],"prediction":[36],"models,":[37],"predicting":[38],"conformations":[39],"resulting":[40],"from":[41],"major":[42,124],"domain":[43,125],"motions":[44,46],"that":[47,66,112],"occur":[48],"over":[49],"long":[50],"timescales":[51],"still":[52],"remains":[53],"a":[54,62],"challenge.":[55],"To":[56],"this":[57],"end,":[58],"we":[59,91],"introduce":[60],"GNMCADS,":[61],"strategy":[65],"enhances":[67],"the":[68,77,82,87,95,101],"diversity":[69,131],"protein":[71,105],"diffusion":[72,96],"models":[73],"selectively":[75],"annealing":[76],"conditioning":[78],"signal":[79],"guided":[80],"intrinsic":[83],"dynamical":[84],"organization":[85],"sampled":[88],"protein.":[89],"Further,":[90],"implement":[92],"GNMCADS":[93,127],"module":[97],"AlphaFold3,":[99],"enabling":[100],"generation":[102],"conformations.":[106],"When":[107],"benchmarked":[108],"across":[109],"92":[110],"proteins":[111,122],"include":[113],"54":[114],"class":[115],"A":[116],"GPCRs,":[117],"15":[118],"transporters,":[119],"and":[120],"23":[121],"with":[123],"movements,":[126],"exhibits":[128],"improved":[129],"compared":[132],"to":[133],"other":[134],"current":[135],"methods.":[138]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-08-30T00:00:00"}
