{"id":"https://openalex.org/W4385345650","doi":"https://doi.org/10.1201/9781003456100-11","title":"Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding","display_name":"Propagation of Conformational Coordinates Across Angular Space in Mapping the Continuum of States from Cryo-EM Data by Manifold Embedding","publication_year":2023,"publication_date":"2023-07-28","ids":{"openalex":"https://openalex.org/W4385345650","doi":"https://doi.org/10.1201/9781003456100-11"},"language":"en","primary_location":{"id":"doi:10.1201/9781003456100-11","doi":"https://doi.org/10.1201/9781003456100-11","is_oa":true,"landing_page_url":"https://doi.org/10.1201/9781003456100-11","pdf_url":"https://api.taylorfrancis.com/content/chapters/edit/download?identifierName=doi&identifierValue=10.1201/9781003456100-11&type=chapterpdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Novel Developments in Cryo\u2010EM of Biological Molecules","raw_type":"book-chapter"},"volume":{"id":"https://openalex.org/W4385345133","display_name":"Novel Developments in Cryo\u2010EM of Biological Molecules"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://api.taylorfrancis.com/content/chapters/edit/download?identifierName=doi&identifierValue=10.1201/9781003456100-11&type=chapterpdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078620906","display_name":"Suvrajit Maji","orcid":"https://orcid.org/0000-0001-5547-1975","observed_orcids":["https://orcid.org/0000-0001-5547-1975"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suvrajit Maji","raw_affiliation_strings":["Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168 th Street, New York, NY 10032, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168 th Street, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022258349","display_name":"Hstau Y. Liao","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hstau Liao","raw_affiliation_strings":["Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168 th Street, New York, NY 10032, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168 th Street, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Ali Dashti","orcid":null,"observed_orcids":[]},"institutions":[{"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":["US"],"is_corresponding":false,"raw_author_name":"Ali Dashti","raw_affiliation_strings":["Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI 53211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI 53211, USA","institution_ids":["https://openalex.org/I43579087"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066902061","display_name":"Ghoncheh Mashayekhi","orcid":"https://orcid.org/0000-0001-9891-190X","observed_orcids":["https://orcid.org/0000-0001-9891-190X"]},"institutions":[{"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":["US"],"is_corresponding":false,"raw_author_name":"Ghoncheh Mashayekhi","raw_affiliation_strings":["Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI 53211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI 53211, USA","institution_ids":["https://openalex.org/I43579087"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046278266","display_name":"A. Ourmazd","orcid":"https://orcid.org/0000-0001-9946-3889","observed_orcids":["https://orcid.org/0000-0001-9946-3889"]},"institutions":[{"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":["US"],"is_corresponding":false,"raw_author_name":"Abbas Ourmazd","raw_affiliation_strings":["Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI 53211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI 53211, USA","institution_ids":["https://openalex.org/I43579087"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042892654","display_name":"Joachim Frank","orcid":"https://orcid.org/0000-0001-5449-6943","observed_orcids":["https://orcid.org/0000-0001-5449-6943","https://orcid.org/0000-0002-2442-1112"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joachim Frank","raw_affiliation_strings":["Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168 th Street, New York, NY 10032, USA","Department of Biological Sciences, Columbia University, 600 Fairchild Center, New York, NY 10027, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168 th Street, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"Department of Biological Sciences, Columbia University, 600 Fairchild Center, New York, NY 10027, USA","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.22580645,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"177","last_page":"198"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.8978999853134155,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.8978999853134155,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T10044","display_name":"Protein Structure and Dynamics","score":0.0828000009059906,"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/T11162","display_name":"Enzyme Structure and Function","score":0.002899999963119626,"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/manifold-embedding","display_name":"manifold embedding","score":0.6830000281333923},{"id":"https://openalex.org/keywords/cryo-electron-microscopy","display_name":"cryo-electron microscopy","score":0.652999997138977},{"id":"https://openalex.org/keywords/single-particle-cryo-electron-microscopy","display_name":"single-particle cryo-electron microscopy","score":0.8019999861717224},{"id":"https://openalex.org/keywords/projection-direction","display_name":"projection direction","score":0.7170000076293945},{"id":"https://openalex.org/keywords/probabilistic-graphical-models","display_name":"probabilistic graphical models","score":0.7459999918937683},{"id":"https://openalex.org/keywords/feature-extraction","display_name":"feature extraction","score":0.8769999742507935},{"id":"https://openalex.org/keywords/energy-landscape","display_name":"energy landscape","score":0.9160000085830688},{"id":"https://openalex.org/keywords/low-dimensional-embedding","display_name":"low-dimensional embedding","score":0.515999972820282}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.7453981637954712},{"id":"https://openalex.org/C529865628","wikidata":"https://www.wikidata.org/wiki/Q1790740","display_name":"Manifold (fluid mechanics)","level":2,"score":0.6189687252044678},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.5083553194999695},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.4599681496620178},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.1667652130126953},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1168750524520874},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.042354315519332886},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1201/9781003456100-11","doi":"https://doi.org/10.1201/9781003456100-11","is_oa":true,"landing_page_url":"https://doi.org/10.1201/9781003456100-11","pdf_url":"https://api.taylorfrancis.com/content/chapters/edit/download?identifierName=doi&identifierValue=10.1201/9781003456100-11&type=chapterpdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Novel Developments in Cryo\u2010EM of Biological Molecules","raw_type":"book-chapter"}],"best_oa_location":{"id":"doi:10.1201/9781003456100-11","doi":"https://doi.org/10.1201/9781003456100-11","is_oa":true,"landing_page_url":"https://doi.org/10.1201/9781003456100-11","pdf_url":"https://api.taylorfrancis.com/content/chapters/edit/download?identifierName=doi&identifierValue=10.1201/9781003456100-11&type=chapterpdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Novel Developments in Cryo\u2010EM of Biological Molecules","raw_type":"book-chapter"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4385345650.pdf","grobid_xml":"https://content.openalex.org/works/W4385345650.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W114565888","https://openalex.org/W1560512119","https://openalex.org/W1578285471","https://openalex.org/W1593793857","https://openalex.org/W1599270913","https://openalex.org/W1823667034","https://openalex.org/W1933157909","https://openalex.org/W1934021597","https://openalex.org/W2024060531","https://openalex.org/W2098678088","https://openalex.org/W2116975878","https://openalex.org/W2120294885","https://openalex.org/W2129031807","https://openalex.org/W2130697955","https://openalex.org/W2137532396","https://openalex.org/W2143516773","https://openalex.org/W2156358825","https://openalex.org/W2159080219","https://openalex.org/W2161969291","https://openalex.org/W2163364417","https://openalex.org/W2167947196","https://openalex.org/W4220975623","https://openalex.org/W4237840503","https://openalex.org/W4241385190","https://openalex.org/W4247880210","https://openalex.org/W4254018622","https://openalex.org/W4292691288","https://openalex.org/W4293052541"],"related_works":["https://openalex.org/W3196874527","https://openalex.org/W7171397391","https://openalex.org/W6902747812","https://openalex.org/W4362684783","https://openalex.org/W4385345062","https://openalex.org/W4385346003","https://openalex.org/W4376130037","https://openalex.org/W4206525227","https://openalex.org/W4408066103","https://openalex.org/W4315478955"],"abstract_inverted_index":{"Recent":[0],"approaches":[1],"to":[2,11,18,42,56,106,116],"the":[3,20,44,57,66,89,92,96,108,130,138],"study":[4,132],"of":[5,22,24,46,65,74,91,133],"biological":[6],"molecules":[7],"employ":[8,113],"manifold":[9,124],"learning":[10],"single-particle":[12],"cryogenic":[13],"electron":[14],"microscopy":[15],"data":[16],"sets":[17],"map":[19],"continuum":[21],"states":[23],"a":[25,28,103],"molecule":[26],"into":[27],"low-dimensional":[29],"space":[30],"spanned":[31],"by":[32],"eigenvectors":[33],"or":[34],"\u201cconformational":[35],"coordinates.\u201d":[36],"This":[37],"chapter":[38,101],"presents":[39],"an":[40,85],"approach":[41],"automate":[43],"propagation":[45,80],"conformational":[47,93,109,135],"coordinates":[48],"across":[49,120],"all":[50],"projection":[51],"directions":[52],"(PDs),":[53],"in":[54,76,95],"contrast":[55],"current":[58],"manual-selection":[59],"approach,":[60],"which":[61],"entails":[62],"user":[63],"inspection":[64],"movies":[67,75,97],"for":[68],"each":[69],"PD":[70],"and":[71,111],"visual":[72],"comparison":[73],"adjacent":[77],"PDs.":[78],"The":[79,100],"process":[81],"is":[82,98],"formulated":[83],"as":[84],"optimization":[86],"problem,":[87],"where":[88],"\u201ccloseness\u201d":[90],"changes":[94],"maximized.":[99],"utilizes":[102],"feature-extraction":[104],"technique":[105,126],"encode":[107],"change":[110],"then":[112],"graphical":[114],"models":[115],"propagate":[117],"this":[118],"information":[119],"angular":[121],"space.":[122],"A":[123],"embedding-based":[125],"recently":[127],"introduced":[128],"enables":[129],"quantitative":[131],"continuous":[134],"motions":[136],"over":[137],"energy":[139],"landscape.":[140]},"counts_by_year":[],"updated_date":"2026-10-30T12:39:25.321706","created_date":"2023-07-29T00:00:00"}
