{"id":"https://openalex.org/W7139949538","doi":"https://doi.org/10.48550/arxiv.2603.18505","title":"From Snapshots to Symphonies: The Evolution of Protein Prediction from Static Structures to Generative Dynamics and Multimodal Interactions","display_name":"From Snapshots to Symphonies: The Evolution of Protein Prediction from Static Structures to Generative Dynamics and Multimodal Interactions","publication_year":2026,"publication_date":"2026-03-19","ids":{"openalex":"https://openalex.org/W7139949538","doi":"https://doi.org/10.48550/arxiv.2603.18505"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2603.18505","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.18505","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2603.18505","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5130240445","display_name":"Jingzhi Chen","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chen, Jingzhi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5130215277","display_name":"Lijian Xu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xu, Lijian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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":0.6111000180244446,"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":0.6111000180244446,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0877000018954277,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.0478999987244606,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.667900025844574},{"id":"https://openalex.org/keywords/transformation","display_name":"Transformation (genetics)","score":0.47929999232292175},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.4790000021457672},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.45890000462532043},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.42750000953674316},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.384799987077713},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"Conformational ensembles","score":0.374099999666214},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.34619998931884766}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.692300021648407},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.667900025844574},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4936999976634979},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.47929999232292175},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.4790000021457672},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.45890000462532043},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.42750000953674316},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.384799987077713},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.374099999666214},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.34619998931884766},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.34470000863075256},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3407000005245209},{"id":"https://openalex.org/C66153294","wikidata":"https://www.wikidata.org/wiki/Q899291","display_name":"CASP","level":4,"score":0.31380000710487366},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.3107999861240387},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.3061000108718872},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.30309998989105225},{"id":"https://openalex.org/C45357846","wikidata":"https://www.wikidata.org/wiki/Q2001982","display_name":"Notation","level":2,"score":0.2955999970436096},{"id":"https://openalex.org/C2992240565","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Protein evolution","level":3,"score":0.2833000123500824},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.26759999990463257},{"id":"https://openalex.org/C2775981520","wikidata":"https://www.wikidata.org/wiki/Q17156992","display_name":"Protein dynamics","level":3,"score":0.25200000405311584},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.251800000667572}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2603.18505","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.18505","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2603.18505","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.18505","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"The":[0],"protein":[1,37,87,89,93,94],"folding":[2],"problem":[3],"has":[4],"been":[5],"fundamentally":[6],"transformed":[7],"by":[8],"artificial":[9,151],"intelligence,":[10],"evolving":[11],"from":[12,154],"static":[13,55],"structure":[14],"prediction":[15,56,82],"toward":[16,134],"the":[17,31,122,169],"modeling":[18],"of":[19,54,83,99,164,172],"dynamic":[20,170],"conformational":[21,76],"ensembles":[22],"and":[23,50,61,71,92,96,104,121,127,142,166],"complex":[24,64],"biomolecular":[25],"interactions.":[26],"This":[27,147],"review":[28],"systematically":[29],"examines":[30],"paradigm":[32],"shift":[33],"in":[34],"AI":[35],"driven":[36],"science":[38],"across":[39],"five":[40],"interconnected":[41],"dimensions:":[42],"unified":[43],"multimodal":[44,139],"representations":[45],"that":[46,74],"integrate":[47],"sequences,":[48],"geometries,":[49],"textual":[51],"knowledge;":[52],"refinement":[53],"through":[57],"MSA":[58],"free":[59],"architectures":[60],"all":[62],"atom":[63],"modeling;":[65],"generative":[66,137],"frameworks,":[67],"including":[68,114],"diffusion":[69],"models":[70],"flow":[72],"matching,":[73],"capture":[75],"distributions":[77],"consistent":[78,136],"with":[79],"thermodynamic":[80],"ensembles;":[81],"heterogeneous":[84],"interactions":[85],"spanning":[86],"ligand,":[88],"nucleic":[90],"acid,":[91],"complexes;":[95],"functional":[97],"inference":[98],"fitness":[100],"landscapes,":[101],"mutational":[102],"effects,":[103],"text":[105],"guided":[106],"property":[107],"prediction.":[108],"We":[109],"critically":[110],"analyze":[111],"current":[112],"bottlenecks,":[113],"data":[115],"distribution":[116],"biases,":[117],"limited":[118],"mechanistic":[119],"interpretability,":[120],"disconnect":[123],"between":[124],"geometric":[125],"metrics":[126],"biophysical":[128],"reality,":[129],"while":[130],"identifying":[131],"future":[132],"directions":[133],"physically":[135],"models,":[138],"foundation":[140],"architectures,":[141],"experimental":[143],"closed":[144],"loop":[145],"systems.":[146],"methodological":[148],"transformation":[149],"marks":[150],"intelligence's":[152],"transition":[153],"a":[155,160],"structural":[156],"analysis":[157],"tool":[158],"into":[159],"universal":[161],"simulator":[162],"capable":[163],"understanding":[165],"ultimately":[167],"rewriting":[168],"language":[171],"life.":[173]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-03-21T00:00:00"}