{"id":"https://openalex.org/W2748411751","doi":"https://doi.org/10.1145/3107411.3107498","title":"Evolving Conformation Paths to Model Protein Structural Transitions","display_name":"Evolving Conformation Paths to Model Protein Structural Transitions","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2748411751","doi":"https://doi.org/10.1145/3107411.3107498","mag":"2748411751"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3107498","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107498","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5105350545","display_name":"Emmanuel Sapin","orcid":"https://orcid.org/0000-0002-7188-3715"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Emmanuel Sapin","raw_affiliation_strings":["George Mason University, Fairfax, VA, USA"],"affiliations":[{"raw_affiliation_string":"George Mason University, Fairfax, VA, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111782149","display_name":"Kenneth De Jong","orcid":"https://orcid.org/0000-0002-2799-280X"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kenneth De Jong","raw_affiliation_strings":["George Mason University, Fairfax, VA, USA"],"affiliations":[{"raw_affiliation_string":"George Mason University, Fairfax, VA, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044722808","display_name":"Amarda Shehu","orcid":"https://orcid.org/0000-0001-5230-4610"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amarda Shehu","raw_affiliation_strings":["George Mason University, Fairfax, VA, USA"],"affiliations":[{"raw_affiliation_string":"George Mason University, Fairfax, VA, USA","institution_ids":["https://openalex.org/I162714631"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5105350545"],"corresponding_institution_ids":["https://openalex.org/I162714631"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.09048563,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"673","last_page":"678"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9957000017166138,"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":0.9865000247955322,"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/energy-landscape","display_name":"Energy landscape","score":0.6779037714004517},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.612284779548645},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.5304992198944092},{"id":"https://openalex.org/keywords/series","display_name":"Series (stratigraphy)","score":0.4660398066043854},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4527660608291626},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4389817714691162},{"id":"https://openalex.org/keywords/fitness-landscape","display_name":"Fitness landscape","score":0.4388042092323303},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4113655686378479},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.38592419028282166},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3720467984676361},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3499380946159363},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3441659212112427},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1809481978416443},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17970791459083557},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1627243459224701},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.15076297521591187},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10237985849380493}],"concepts":[{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.6779037714004517},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.612284779548645},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.5304992198944092},{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.4660398066043854},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4527660608291626},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4389817714691162},{"id":"https://openalex.org/C91852762","wikidata":"https://www.wikidata.org/wiki/Q3307742","display_name":"Fitness landscape","level":3,"score":0.4388042092323303},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4113655686378479},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.38592419028282166},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3720467984676361},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3499380946159363},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3441659212112427},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1809481978416443},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17970791459083557},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1627243459224701},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.15076297521591187},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10237985849380493},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3107411.3107498","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107498","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.7300000190734863,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G7125901736","display_name":null,"funder_award_id":"1421001, 1144106","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W626438322","https://openalex.org/W848174273","https://openalex.org/W1798761798","https://openalex.org/W1876787341","https://openalex.org/W1995808589","https://openalex.org/W2016423785","https://openalex.org/W2034801091","https://openalex.org/W2048822589","https://openalex.org/W2072090246","https://openalex.org/W2077743314","https://openalex.org/W2094795801","https://openalex.org/W2100091931","https://openalex.org/W2103237643","https://openalex.org/W2114229182","https://openalex.org/W2127362915","https://openalex.org/W2128736063","https://openalex.org/W2161748992","https://openalex.org/W2171755502","https://openalex.org/W2200755474","https://openalex.org/W2201713963","https://openalex.org/W2296721019","https://openalex.org/W2343931134","https://openalex.org/W2462141059","https://openalex.org/W2463055951","https://openalex.org/W2504277605","https://openalex.org/W2509964510","https://openalex.org/W2552685162","https://openalex.org/W2559246072"],"related_works":["https://openalex.org/W4322621737","https://openalex.org/W1984474632","https://openalex.org/W1997080762","https://openalex.org/W2018853124","https://openalex.org/W2044897135","https://openalex.org/W1970185413","https://openalex.org/W2979798330","https://openalex.org/W4391323729","https://openalex.org/W4385836827","https://openalex.org/W2044498124"],"abstract_inverted_index":{"Proteins":[0],"are":[1],"dynamic":[2],"biomolecules.":[3],"A":[4],"structure-by-structure":[5],"characterization":[6],"of":[7,22,46,53,67,74,81,89,128],"a":[8,54,94,132,144],"protein's":[9],"transition":[10],"between":[11],"two":[12,109],"different":[13],"functional":[14],"structures":[15,52,73],"is":[16,139],"central":[17],"to":[18,130],"elucidating":[19],"the":[20,47,79,87,105,123,137],"role":[21],"dynamics":[23],"in":[24],"modulating":[25],"protein":[26,55,83],"function":[27],"and":[28,37,71,92,115],"designing":[29],"therapeutic":[30],"drugs.":[31],"Characterizing":[32],"transitions":[33,85],"challenges":[34],"both":[35],"dry":[36],"wet":[38],"laboratories.":[39],"Some":[40],"computational":[41,146],"methods":[42],"compute":[43],"discrete":[44],"representations":[45,61],"energy":[48,106],"landscape":[49],"that":[50],"organizes":[51],"by":[56],"their":[57],"potential":[58],"energies.":[59],"The":[60,99],"support":[62],"queries":[63],"for":[64],"paths":[65,102,129],"(series":[66],"structures)":[68],"connecting":[69],"start":[70],"goal":[72],"interest.":[75],"Here":[76],"we":[77],"address":[78],"problem":[80],"modeling":[82],"structural":[84,116],"under":[86,143],"umbrella":[88],"stochastic":[90],"optimization":[91,111],"propose":[93],"novel":[95],"evolutionary":[96],"algorithm":[97],"(EA).":[98],"EA":[100,124,138],"evolves":[101],"without":[103],"reconstructing":[104],"landscape,":[107],"addressing":[108],"competing":[110],"objectives,":[112],"energetic":[113],"cost":[114],"resolution.":[117],"Rather":[118],"than":[119],"seek":[120],"one":[121],"path,":[122],"yields":[125],"an":[126],"ensemble":[127],"represent":[131],"transition.":[133],"Preliminary":[134],"applications":[135],"suggest":[136],"effective":[140],"while":[141],"operating":[142],"reasonable":[145],"budget.":[147]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}