{"id":"https://openalex.org/W4321610320","doi":"https://doi.org/10.1021/acs.jcim.2c01444","title":"Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation","display_name":"Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation","publication_year":2023,"publication_date":"2023-02-23","ids":{"openalex":"https://openalex.org/W4321610320","doi":"https://doi.org/10.1021/acs.jcim.2c01444","pmid":"https://pubmed.ncbi.nlm.nih.gov/36821519"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c01444","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01444","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.2c01444","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.2c01444","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017088569","display_name":"Yutaka Maruyama","orcid":"https://orcid.org/0000-0003-4035-4885"},"institutions":[{"id":"https://openalex.org/I146230289","display_name":"Omron (Japan)","ror":"https://ror.org/00q0w1h45","country_code":"JP","type":"company","lineage":["https://openalex.org/I146230289"]},{"id":"https://openalex.org/I16656306","display_name":"Meiji University","ror":"https://ror.org/02rqvrp93","country_code":"JP","type":"education","lineage":["https://openalex.org/I16656306"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yutaka Maruyama","raw_affiliation_strings":["Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan","OMRON SINIC X Corporation, Tokyo 113-0033, Japan"],"raw_orcid":"https://orcid.org/0000-0003-4035-4885","affiliations":[{"raw_affiliation_string":"Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan","institution_ids":["https://openalex.org/I16656306"]},{"raw_affiliation_string":"OMRON SINIC X Corporation, Tokyo 113-0033, Japan","institution_ids":["https://openalex.org/I146230289"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066135113","display_name":"Ryo Igarashi","orcid":"https://orcid.org/0000-0002-2894-7226"},"institutions":[{"id":"https://openalex.org/I146230289","display_name":"Omron (Japan)","ror":"https://ror.org/00q0w1h45","country_code":"JP","type":"company","lineage":["https://openalex.org/I146230289"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ryo Igarashi","raw_affiliation_strings":["OMRON SINIC X Corporation, Tokyo 113-0033, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"OMRON SINIC X Corporation, Tokyo 113-0033, Japan","institution_ids":["https://openalex.org/I146230289"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077707500","display_name":"Yoshitaka Ushiku","orcid":"https://orcid.org/0000-0002-9014-1389"},"institutions":[{"id":"https://openalex.org/I146230289","display_name":"Omron (Japan)","ror":"https://ror.org/00q0w1h45","country_code":"JP","type":"company","lineage":["https://openalex.org/I146230289"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshitaka Ushiku","raw_affiliation_strings":["OMRON SINIC X Corporation, Tokyo 113-0033, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"OMRON SINIC X Corporation, Tokyo 113-0033, Japan","institution_ids":["https://openalex.org/I146230289"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047988646","display_name":"Ayori Mitsutake","orcid":"https://orcid.org/0000-0002-4194-7255"},"institutions":[{"id":"https://openalex.org/I16656306","display_name":"Meiji University","ror":"https://ror.org/02rqvrp93","country_code":"JP","type":"education","lineage":["https://openalex.org/I16656306"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ayori Mitsutake","raw_affiliation_strings":["Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan"],"raw_orcid":"https://orcid.org/0000-0002-4194-7255","affiliations":[{"raw_affiliation_string":"Department of Physics, School of Science and Technology, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki-shi, Kanagawa 214-8571, Japan","institution_ids":["https://openalex.org/I16656306"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017088569"],"corresponding_institution_ids":["https://openalex.org/I146230289","https://openalex.org/I16656306"],"apc_list":null,"apc_paid":null,"fwci":17.054,"has_fulltext":true,"cited_by_count":187,"citation_normalized_percentile":{"value":0.99650247,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"63","issue":"5","first_page":"1529","last_page":"1541"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9958000183105469,"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"}},{"id":"https://openalex.org/T10303","display_name":"Photosynthetic Processes and Mechanisms","score":0.9948999881744385,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/root-mean-square","display_name":"Root mean square","score":0.8410874605178833},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.6519694328308105},{"id":"https://openalex.org/keywords/metastability","display_name":"Metastability","score":0.5659531950950623},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.515021562576294},{"id":"https://openalex.org/keywords/absolute-deviation","display_name":"Absolute deviation","score":0.4575596749782562},{"id":"https://openalex.org/keywords/interval","display_name":"Interval (graph theory)","score":0.4476800560951233},{"id":"https://openalex.org/keywords/mean-squared-error","display_name":"Mean squared error","score":0.4383803606033325},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.43103379011154175},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.41671621799468994},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.4016069173812866},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.375166654586792},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.343024879693985},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2848609387874603},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.24838796257972717},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.1709301769733429},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.0937201976776123},{"id":"https://openalex.org/keywords/structural-engineering","display_name":"Structural engineering","score":0.07527786493301392}],"concepts":[{"id":"https://openalex.org/C71907059","wikidata":"https://www.wikidata.org/wiki/Q223323","display_name":"Root mean square","level":2,"score":0.8410874605178833},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6519694328308105},{"id":"https://openalex.org/C89464430","wikidata":"https://www.wikidata.org/wiki/Q849516","display_name":"Metastability","level":2,"score":0.5659531950950623},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.515021562576294},{"id":"https://openalex.org/C120934525","wikidata":"https://www.wikidata.org/wiki/Q849149","display_name":"Absolute deviation","level":2,"score":0.4575596749782562},{"id":"https://openalex.org/C2778067643","wikidata":"https://www.wikidata.org/wiki/Q166507","display_name":"Interval (graph theory)","level":2,"score":0.4476800560951233},{"id":"https://openalex.org/C139945424","wikidata":"https://www.wikidata.org/wiki/Q1940696","display_name":"Mean squared error","level":2,"score":0.4383803606033325},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.43103379011154175},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.41671621799468994},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.4016069173812866},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.375166654586792},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.343024879693985},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2848609387874603},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.24838796257972717},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.1709301769733429},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0937201976776123},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.07527786493301392},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"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/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.2c01444","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01444","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.2c01444","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:36821519","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36821519","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10015464","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10015464","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10015464/pdf/ci2c01444.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.2c01444","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01444","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.2c01444","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1523338652","display_name":"Construction and application of a computational system for evaluating stability and function of protein due to amino acid substitution","funder_award_id":"23K20301","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G2959223040","display_name":null,"funder_award_id":"JP20H03230","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5137156025","display_name":null,"funder_award_id":"22H04756","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5312568430","display_name":null,"funder_award_id":"JPMJMI19G1","funder_id":"https://openalex.org/F4320338243","funder_display_name":"JST-Mirai Program"},{"id":"https://openalex.org/G8431728377","display_name":"\u6570\u7406\u79d1\u5b66\u3092\u6d3b\u7528\u3057\u305f\u30de\u30eb\u30c1\u30b9\u30b1\u30fc\u30eb\u30fb\u30de\u30eb\u30c1\u30e2\u30fc\u30c0\u30eb\u69cb\u9020\u89e3\u6790\u30b7\u30b9\u30c6\u30e0","funder_award_id":"JPMJMI19G1","funder_id":"https://openalex.org/F4320334789","funder_display_name":"Japan Science and Technology Agency"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320338243","display_name":"JST-Mirai Program","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4321610320.pdf","grobid_xml":"https://content.openalex.org/works/W4321610320.grobid-xml"},"referenced_works_count":105,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1482971402","https://openalex.org/W1570122994","https://openalex.org/W1797445294","https://openalex.org/W1895692106","https://openalex.org/W1926968922","https://openalex.org/W1945663778","https://openalex.org/W1965016619","https://openalex.org/W1972764810","https://openalex.org/W1986315017","https://openalex.org/W1987161922","https://openalex.org/W1992921903","https://openalex.org/W1995907662","https://openalex.org/W2000702472","https://openalex.org/W2004822259","https://openalex.org/W2005601729","https://openalex.org/W2006056376","https://openalex.org/W2007361250","https://openalex.org/W2007662810","https://openalex.org/W2008232194","https://openalex.org/W2019291826","https://openalex.org/W2026569704","https://openalex.org/W2027109368","https://openalex.org/W2027408247","https://openalex.org/W2027835075","https://openalex.org/W2028263411","https://openalex.org/W2032229140","https://openalex.org/W2032398506","https://openalex.org/W2042490093","https://openalex.org/W2042947255","https://openalex.org/W2046898277","https://openalex.org/W2050333027","https://openalex.org/W2055564206","https://openalex.org/W2056910212","https://openalex.org/W2060199905","https://openalex.org/W2060757799","https://openalex.org/W2064090886","https://openalex.org/W2065919348","https://openalex.org/W2067236515","https://openalex.org/W2068540815","https://openalex.org/W2069288013","https://openalex.org/W2071739952","https://openalex.org/W2074597624","https://openalex.org/W2075788626","https://openalex.org/W2082586732","https://openalex.org/W2084800760","https://openalex.org/W2091701505","https://openalex.org/W2103743266","https://openalex.org/W2107851313","https://openalex.org/W2111527085","https://openalex.org/W2131560721","https://openalex.org/W2132629607","https://openalex.org/W2142578757","https://openalex.org/W2143592395","https://openalex.org/W2155948223","https://openalex.org/W2159497832","https://openalex.org/W2159923313","https://openalex.org/W2160400329","https://openalex.org/W2160544821","https://openalex.org/W2165414288","https://openalex.org/W2170711116","https://openalex.org/W2171144241","https://openalex.org/W2180785390","https://openalex.org/W2257585669","https://openalex.org/W2279218789","https://openalex.org/W2312553612","https://openalex.org/W2313116527","https://openalex.org/W2315297180","https://openalex.org/W2320634206","https://openalex.org/W2326832031","https://openalex.org/W2343852072","https://openalex.org/W2398566557","https://openalex.org/W2489582920","https://openalex.org/W2534969466","https://openalex.org/W2554914124","https://openalex.org/W2583392439","https://openalex.org/W2762283147","https://openalex.org/W2771272808","https://openalex.org/W2792314036","https://openalex.org/W2792802992","https://openalex.org/W2800801983","https://openalex.org/W2807208633","https://openalex.org/W2917952902","https://openalex.org/W2944621351","https://openalex.org/W2954443325","https://openalex.org/W2964741900","https://openalex.org/W2968572727","https://openalex.org/W2969816247","https://openalex.org/W2978380288","https://openalex.org/W2986430220","https://openalex.org/W2990103831","https://openalex.org/W2991078804","https://openalex.org/W3026208107","https://openalex.org/W3034615909","https://openalex.org/W3046751266","https://openalex.org/W3097616367","https://openalex.org/W3100810942","https://openalex.org/W3103156673","https://openalex.org/W3105575067","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3196265092","https://openalex.org/W3216238908","https://openalex.org/W4212978540","https://openalex.org/W4289948291"],"related_works":["https://openalex.org/W2260493136","https://openalex.org/W2113188411","https://openalex.org/W2976965029","https://openalex.org/W2382178265","https://openalex.org/W2055827177","https://openalex.org/W2072666835","https://openalex.org/W4248706500","https://openalex.org/W1999927713","https://openalex.org/W2939859775","https://openalex.org/W4252654006"],"abstract_inverted_index":{"We":[0,48,103],"apply":[1],"moving":[2],"root-mean-square":[3,28],"deviation":[4,29],"(mRMSD),":[5],"which":[6,84],"does":[7],"not":[8],"require":[9],"a":[10,14,80],"reference":[11],"structure,":[12],"as":[13,70,72],"method":[15,21,51,122,146],"for":[16],"analyzing":[17],"protein":[18,41,116],"dynamics.":[19],"This":[20,145],"can":[22,130,147],"be":[23,131,148],"used":[24,132],"to":[25,39,52,114,123,133,141,150],"calculate":[26],"the":[27,53,58,73,85,96,101,142],"(RMSD)":[30],"of":[31,67,88,100,136,154],"structure":[32,82,99],"between":[33],"two":[34],"specified":[35],"time":[36,45,112],"points":[37],"and":[38,61,90],"analyze":[40],"dynamics":[42,117,152],"behavior":[43],"through":[44],"series":[46],"analysis.":[47],"applied":[49,149],"this":[50,121],"Trp-cage":[54],"trajectory":[55],"calculated":[56],"by":[57],"Anton":[59],"supercomputer":[60],"found":[62,127],"that":[63,106,128],"it":[64],"shows":[65],"regions":[66,135],"stable":[68,98,143,157],"states":[69,138],"well":[71],"conventional":[74],"RMSD.":[75],"In":[76],"addition,":[77],"we":[78,126],"extracted":[79],"characteristic":[81],"in":[83,139],"side":[86],"chains":[87],"Asp1":[89],"Arg16":[91],"form":[92],"hydrogen":[93],"bonds":[94],"near":[95],"most":[97],"Trp-cage.":[102],"also":[104],"determined":[105],"\u226520":[107],"ns":[108],"is":[109],"an":[110],"appropriate":[111],"interval":[113],"investigate":[115],"using":[118],"mRMSD.":[119],"Applying":[120],"NuG2":[124],"protein,":[125],"mRMSD":[129],"detect":[134],"metastable":[137],"addition":[140],"state.":[144],"molecular":[151],"simulations":[153],"proteins":[155],"whose":[156],"structures":[158],"are":[159],"unknown.":[160]},"counts_by_year":[{"year":2026,"cited_by_count":61},{"year":2025,"cited_by_count":77},{"year":2024,"cited_by_count":38},{"year":2023,"cited_by_count":11}],"updated_date":"2026-08-16T07:02:28.622633","created_date":"2025-10-10T00:00:00"}
