{"id":"https://openalex.org/W2796160261","doi":"https://doi.org/10.1145/3180382.3180390","title":"Coarse-Grained Molecular Dynamics Simulation of Sulerythrin and LARFH for Producing Protein Nanofibers","display_name":"Coarse-Grained Molecular Dynamics Simulation of Sulerythrin and LARFH for Producing Protein Nanofibers","publication_year":2018,"publication_date":"2018-01-18","ids":{"openalex":"https://openalex.org/W2796160261","doi":"https://doi.org/10.1145/3180382.3180390","mag":"2796160261"},"language":"en","primary_location":{"id":"doi:10.1145/3180382.3180390","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3180382.3180390","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics","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/A5105210993","display_name":"Takashi Ozawa","orcid":null},"institutions":[{"id":"https://openalex.org/I149964584","display_name":"Tokyo University of Pharmacy and Life Sciences","ror":"https://ror.org/057jm7w82","country_code":"JP","type":"education","lineage":["https://openalex.org/I149964584"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Takashi Ozawa","raw_affiliation_strings":["Computational Biophysics Laboratory, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Computational Biophysics Laboratory, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan","institution_ids":["https://openalex.org/I149964584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006732886","display_name":"H. Yamada","orcid":"https://orcid.org/0000-0002-5686-1657"},"institutions":[{"id":"https://openalex.org/I4210134673","display_name":"The Institute of Statistical Mathematics","ror":"https://ror.org/03jcejr58","country_code":"JP","type":"facility","lineage":["https://openalex.org/I1319490839","https://openalex.org/I4210134673","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hironao Yamada","raw_affiliation_strings":["The Institute of Statistical Mathematics, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"The Institute of Statistical Mathematics, Tokyo, Japan","institution_ids":["https://openalex.org/I4210134673"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106858380","display_name":"Takeshi Miyakawa","orcid":null},"institutions":[{"id":"https://openalex.org/I149964584","display_name":"Tokyo University of Pharmacy and Life Sciences","ror":"https://ror.org/057jm7w82","country_code":"JP","type":"education","lineage":["https://openalex.org/I149964584"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takeshi Miyakawa","raw_affiliation_strings":["Computational Biophysics Laboratory, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Computational Biophysics Laboratory, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan","institution_ids":["https://openalex.org/I149964584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070949755","display_name":"Ryota Morikawa","orcid":"https://orcid.org/0000-0001-9958-9756"},"institutions":[{"id":"https://openalex.org/I149964584","display_name":"Tokyo University of Pharmacy and Life Sciences","ror":"https://ror.org/057jm7w82","country_code":"JP","type":"education","lineage":["https://openalex.org/I149964584"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ryota Morikawa","raw_affiliation_strings":["Computational Biophysics Laboratory, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Computational Biophysics Laboratory, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan","institution_ids":["https://openalex.org/I149964584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012161036","display_name":"Sota Yagi","orcid":"https://orcid.org/0000-0002-7117-3318"},"institutions":[{"id":"https://openalex.org/I149964584","display_name":"Tokyo University of Pharmacy and Life Sciences","ror":"https://ror.org/057jm7w82","country_code":"JP","type":"education","lineage":["https://openalex.org/I149964584"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Sota Yagi","raw_affiliation_strings":["Extreme Environmental Biology Laboratory, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Extreme Environmental Biology Laboratory, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan","institution_ids":["https://openalex.org/I149964584"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057837432","display_name":"Satoshi Akanuma","orcid":"https://orcid.org/0000-0002-7584-8570"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Satoshi Akanuma","raw_affiliation_strings":["Waseda University, Saitama, Japan"],"affiliations":[{"raw_affiliation_string":"Waseda University, Saitama, Japan","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035275795","display_name":"Akihiko Yamagishi","orcid":"https://orcid.org/0000-0001-5162-3927"},"institutions":[{"id":"https://openalex.org/I149964584","display_name":"Tokyo University of Pharmacy and Life Sciences","ror":"https://ror.org/057jm7w82","country_code":"JP","type":"education","lineage":["https://openalex.org/I149964584"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akihiko Yamagishi","raw_affiliation_strings":["Extreme Environmental Biology Laboratory, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Extreme Environmental Biology Laboratory, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan","institution_ids":["https://openalex.org/I149964584"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062601176","display_name":"Masako Takasu","orcid":"https://orcid.org/0000-0001-8414-9061"},"institutions":[{"id":"https://openalex.org/I149964584","display_name":"Tokyo University of Pharmacy and Life Sciences","ror":"https://ror.org/057jm7w82","country_code":"JP","type":"education","lineage":["https://openalex.org/I149964584"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masako Takasu","raw_affiliation_strings":["Computational Biophysics Laboratory, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Computational Biophysics Laboratory, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan","institution_ids":["https://openalex.org/I149964584"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5105210993"],"corresponding_institution_ids":["https://openalex.org/I149964584"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.02176683,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"4","issue":null,"first_page":"43","last_page":"47"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9898999929428101,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9898999929428101,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9574999809265137,"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":0.949999988079071,"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/molecular-dynamics","display_name":"Molecular dynamics","score":0.7181083559989929},{"id":"https://openalex.org/keywords/nanobiotechnology","display_name":"Nanobiotechnology","score":0.7040566205978394},{"id":"https://openalex.org/keywords/nanofiber","display_name":"Nanofiber","score":0.6840760707855225},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.5606050491333008},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.5418201088905334},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.4843236207962036},{"id":"https://openalex.org/keywords/atomic-force-microscopy","display_name":"Atomic force microscopy","score":0.4789220094680786},{"id":"https://openalex.org/keywords/branching","display_name":"Branching (polymer chemistry)","score":0.4615263044834137},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.45030295848846436},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4326326251029968},{"id":"https://openalex.org/keywords/molecular-biophysics","display_name":"Molecular biophysics","score":0.4222184419631958},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.37245973944664},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.16626739501953125},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16324129700660706},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14756840467453003},{"id":"https://openalex.org/keywords/nanoparticle","display_name":"Nanoparticle","score":0.13902121782302856}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7181083559989929},{"id":"https://openalex.org/C26926545","wikidata":"https://www.wikidata.org/wiki/Q1939992","display_name":"Nanobiotechnology","level":3,"score":0.7040566205978394},{"id":"https://openalex.org/C91129048","wikidata":"https://www.wikidata.org/wiki/Q594196","display_name":"Nanofiber","level":2,"score":0.6840760707855225},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.5606050491333008},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.5418201088905334},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4843236207962036},{"id":"https://openalex.org/C102951782","wikidata":"https://www.wikidata.org/wiki/Q49295","display_name":"Atomic force microscopy","level":2,"score":0.4789220094680786},{"id":"https://openalex.org/C206175624","wikidata":"https://www.wikidata.org/wiki/Q595731","display_name":"Branching (polymer chemistry)","level":2,"score":0.4615263044834137},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.45030295848846436},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4326326251029968},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.4222184419631958},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.37245973944664},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.16626739501953125},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16324129700660706},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14756840467453003},{"id":"https://openalex.org/C155672457","wikidata":"https://www.wikidata.org/wiki/Q61231","display_name":"Nanoparticle","level":2,"score":0.13902121782302856},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3180382.3180390","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3180382.3180390","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2018 8th International Conference on Bioscience, Biochemistry and Bioinformatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1966078827","https://openalex.org/W1966381151","https://openalex.org/W1981021420","https://openalex.org/W2015642465","https://openalex.org/W2051864856","https://openalex.org/W2092576441","https://openalex.org/W2113495611","https://openalex.org/W2119267663","https://openalex.org/W2123768693","https://openalex.org/W2132184418","https://openalex.org/W2138905138","https://openalex.org/W2160544821","https://openalex.org/W2163552994","https://openalex.org/W2171268876","https://openalex.org/W2262039731"],"related_works":["https://openalex.org/W2557483217","https://openalex.org/W2763600075","https://openalex.org/W2886437959","https://openalex.org/W4210421408","https://openalex.org/W4317767715","https://openalex.org/W2009404409","https://openalex.org/W4229581737","https://openalex.org/W2339278149","https://openalex.org/W2114931176","https://openalex.org/W4286862303"],"abstract_inverted_index":{"Artificial":[0],"creation":[1],"of":[2,10,24,60,76,95,103],"fibers":[3,20],"utilizing":[4],"proteins":[5],"has":[6],"been":[7],"a":[8,93],"target":[9],"bionanotechnology.":[11],"Yagi":[12],"et":[13],"al.":[14],"succeeded":[15],"in":[16,54],"designing":[17],"artificial":[18],"protein":[19],"using":[21,82],"two":[22,104],"types":[23],"proteins:":[25],"LARFH":[26,36,80,109],"and":[27,35,40,73,79,98,101,107],"sulerythrin.":[28],"Binding":[29,88],"interfaces":[30],"were":[31,44,90],"designed":[32,130],"for":[33,92],"sulerythrin":[34,77,97,105,120],"by":[37,46,119],"introducing":[38],"mutations,":[39],"the":[41,55,64,71,129],"fibrous":[42,56],"structures":[43],"confirmed":[45],"atomic":[47],"force":[48],"microscopy.":[49],"However,":[50],"branching":[51],"was":[52],"observed":[53],"structure,":[57],"possibly":[58],"because":[59],"non-specific":[61,123],"interactions":[62],"between":[63],"proteins.":[65],"In":[66],"this":[67],"study,":[68],"we":[69],"analyzed":[70],"behavior":[72],"binding":[74,124],"sites":[75,126],"mutants":[78,81],"coarse-grained":[83],"molecular":[84],"dynamics":[85],"(MD)":[86],"simulation.":[87],"simulations":[89],"performed":[91],"system":[94],"one":[96,99],"LARFH,":[100],"also":[102],"molecules":[106],"four":[108],"molecules.":[110],"These":[111],"results":[112],"suggested":[113],"that":[114],"glutamic":[115],"acids":[116],"originally":[117],"possessed":[118],"contribute":[121],"to":[122],"at":[125],"other":[127],"than":[128],"interfaces.":[131]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}