{"id":"https://openalex.org/W2588644249","doi":"https://doi.org/10.1021/acs.jcim.6b00516","title":"<i>aRMSD</i>: A Comprehensive Tool for Structural Analysis","display_name":"<i>aRMSD</i>: A Comprehensive Tool for Structural Analysis","publication_year":2017,"publication_date":"2017-02-13","ids":{"openalex":"https://openalex.org/W2588644249","doi":"https://doi.org/10.1021/acs.jcim.6b00516","mag":"2588644249","pmid":"https://pubmed.ncbi.nlm.nih.gov/28191844"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00516","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00516","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013397104","display_name":"Arne Wagner","orcid":"https://orcid.org/0000-0002-4232-7015"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Arne Wagner","raw_affiliation_strings":["Institute of Inorganic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-4232-7015","affiliations":[{"raw_affiliation_string":"Institute of Inorganic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073407894","display_name":"Hans\u2010J\u00f6rg Himmel","orcid":"https://orcid.org/0000-0001-8111-3047"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Hans-J\u00f6rg Himmel","raw_affiliation_strings":["Institute of Inorganic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Inorganic Chemistry, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5013397104"],"corresponding_institution_ids":["https://openalex.org/I223822909"],"apc_list":null,"apc_paid":null,"fwci":1.3749,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.82085096,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"57","issue":"3","first_page":"428","last_page":"438"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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"}},{"id":"https://openalex.org/T12852","display_name":"Chemical Thermodynamics and Molecular Structure","score":0.9921000003814697,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12748","display_name":"Molecular spectroscopy and chirality","score":0.9648000001907349,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6201236844062805},{"id":"https://openalex.org/keywords/weighting","display_name":"Weighting","score":0.6077309250831604},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.605868935585022},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5811501145362854},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5527434349060059},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5514553189277649},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.543882429599762},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4751453399658203},{"id":"https://openalex.org/keywords/structural-complexity","display_name":"Structural complexity","score":0.42869675159454346},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.42468297481536865},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4166316092014313},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3554326891899109},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19548648595809937},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.15449467301368713},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.14047974348068237},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10079854726791382}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6201236844062805},{"id":"https://openalex.org/C183115368","wikidata":"https://www.wikidata.org/wiki/Q856577","display_name":"Weighting","level":2,"score":0.6077309250831604},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.605868935585022},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5811501145362854},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5527434349060059},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5514553189277649},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.543882429599762},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4751453399658203},{"id":"https://openalex.org/C509619924","wikidata":"https://www.wikidata.org/wiki/Q17130757","display_name":"Structural complexity","level":2,"score":0.42869675159454346},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.42468297481536865},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4166316092014313},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3554326891899109},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19548648595809937},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.15449467301368713},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.14047974348068237},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10079854726791382},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003300","descriptor_name":"Copper","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003300","descriptor_name":"Copper","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003300","descriptor_name":"Copper","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019791","descriptor_name":"Guanidine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019791","descriptor_name":"Guanidine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019791","descriptor_name":"Guanidine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.6b00516","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00516","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:28191844","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28191844","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1617536095","https://openalex.org/W1965696122","https://openalex.org/W1969404979","https://openalex.org/W1976909321","https://openalex.org/W1986806641","https://openalex.org/W1993267444","https://openalex.org/W1993492933","https://openalex.org/W1994349207","https://openalex.org/W2002596742","https://openalex.org/W2005871523","https://openalex.org/W2010999909","https://openalex.org/W2011301426","https://openalex.org/W2032647355","https://openalex.org/W2035626822","https://openalex.org/W2037406737","https://openalex.org/W2038764332","https://openalex.org/W2041670460","https://openalex.org/W2059457452","https://openalex.org/W2063622629","https://openalex.org/W2064576005","https://openalex.org/W2067718414","https://openalex.org/W2070942956","https://openalex.org/W2077743314","https://openalex.org/W2081287834","https://openalex.org/W2085732173","https://openalex.org/W2087599743","https://openalex.org/W2089447985","https://openalex.org/W2095678277","https://openalex.org/W2104266030","https://openalex.org/W2105159433","https://openalex.org/W2108107014","https://openalex.org/W2110114082","https://openalex.org/W2110283222","https://openalex.org/W2112411768","https://openalex.org/W2116643156","https://openalex.org/W2122576346","https://openalex.org/W2125223656","https://openalex.org/W2125696348","https://openalex.org/W2128175348","https://openalex.org/W2129404618","https://openalex.org/W2130696395","https://openalex.org/W2136567909","https://openalex.org/W2138871907","https://openalex.org/W2139731838","https://openalex.org/W2141461755","https://openalex.org/W2146292423","https://openalex.org/W2158024647","https://openalex.org/W2165434144","https://openalex.org/W2169678694","https://openalex.org/W2169858698","https://openalex.org/W2220239985","https://openalex.org/W2222512263","https://openalex.org/W2325623133","https://openalex.org/W2433293475","https://openalex.org/W2501164770","https://openalex.org/W2950798877","https://openalex.org/W2951528848","https://openalex.org/W4240670390"],"related_works":["https://openalex.org/W2180954594","https://openalex.org/W2052835778","https://openalex.org/W2049003611","https://openalex.org/W2108418243","https://openalex.org/W2127804977","https://openalex.org/W164103134","https://openalex.org/W2787352659","https://openalex.org/W2487162673","https://openalex.org/W1970611213","https://openalex.org/W2793211469"],"abstract_inverted_index":{"A":[0,124],"new":[1,13,125],"free":[2],"tool":[3],"for":[4,76,95,111,117],"structural":[5,135,146,171],"comparison":[6],"is":[7,60,137,140],"presented":[8,138],"that":[9,44,130,159],"combines":[10,131],"existing":[11],"and":[12,36,79,101,104,148,173,179],"features":[14],"into":[15,65],"a":[16,26],"single":[17],"software":[18],"package.":[19],"aRMSD":[20,153],"incorporates":[21],"the":[22,30,37,40,46,51,56,96,105,112,143,162,168,175,187],"functions":[23,91],"of":[24,32,39,55,82,98,107,114,134,145,152,170,177,186],"establishing":[25],"pairwise":[27],"correlation":[28,176],"between":[29,50],"atoms":[31],"two":[33],"molecular":[34],"structures":[35],"calculation":[38,97,113],"optimal":[41],"rotation":[42],"matrix":[43],"minimizes":[45],"root-mean-square":[47],"deviation":[48],"(RMSD)":[49],"molecules.":[52,182],"The":[53,150,183],"complexity":[54],"Hungarian":[57],"assignation":[58],"problem":[59],"reduced":[61],"by":[62,156],"decomposing":[63],"molecules":[64,84],"different":[66,70,87],"subsets":[67],"based":[68],"on":[69],"atom":[71],"or":[72],"group":[73],"types":[74],"allowing":[75],"an":[77],"efficient":[78],"robust":[80],"treatment":[81],"large":[83],"while":[85],"tolerating":[86],"substituents.":[88],"Various":[89],"weighting":[90],"can":[92,164,189],"be":[93,165,190],"used":[94],"RMSD":[99],"values":[100],"similarity":[102,147],"descriptors,":[103],"utilization":[106],"coordinate":[108],"uncertainties":[109],"allows":[110],"standard":[115],"deviations":[116],"all":[118],"calculated":[119],"properties":[120],"through":[121],"error":[122],"propagation.":[123],"three-dimensional":[126],"(3D)":[127],"graphical":[128],"representation":[129],"multiple":[132],"aspects":[133],"information":[136],"which":[139],"useful":[141],"in":[142,167,174,181],"analysis":[144,169],"diversity.":[149],"capabilities":[151],"are":[154],"demonstrated":[155],"selected":[157],"examples":[158],"show":[160],"how":[161],"program":[163,188],"utilized":[166],"changes":[172],"structure":[178],"activity":[180],"source":[184],"code":[185],"downloaded":[191],"at":[192],"https://github.com/armsd/aRMSD":[193],".":[194]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2017-02-24T00:00:00"}
