{"id":"https://openalex.org/W4220671126","doi":"https://doi.org/10.1021/acs.jcim.1c01219","title":"<tt>PoreMatMod.jl</tt> : Julia Package for <i>in Silico</i> Postsynthetic Modification of Crystal Structure Models","display_name":"<tt>PoreMatMod.jl</tt> : Julia Package for <i>in Silico</i> Postsynthetic Modification of Crystal Structure Models","publication_year":2022,"publication_date":"2022-01-14","ids":{"openalex":"https://openalex.org/W4220671126","doi":"https://doi.org/10.1021/acs.jcim.1c01219","pmid":"https://pubmed.ncbi.nlm.nih.gov/35029112"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c01219","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c01219","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/A5060409538","display_name":"E. Adrian Henle","orcid":"https://orcid.org/0000-0002-3331-7173"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"E. Adrian Henle","raw_affiliation_strings":["School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon 97331, United States"],"affiliations":[{"raw_affiliation_string":"School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon 97331, United States","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008498812","display_name":"Nickolas Gantzler","orcid":"https://orcid.org/0000-0003-3832-4994"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nickolas Gantzler","raw_affiliation_strings":["Department of Physics, Oregon State University, Corvallis, Oregon 97331, United States"],"affiliations":[{"raw_affiliation_string":"Department of Physics, Oregon State University, Corvallis, Oregon 97331, United States","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021103322","display_name":"Praveen K. Thallapally","orcid":"https://orcid.org/0000-0001-7814-4467"},"institutions":[{"id":"https://openalex.org/I142606810","display_name":"Pacific Northwest National Laboratory","ror":"https://ror.org/05h992307","country_code":"US","type":"facility","lineage":["https://openalex.org/I1325736334","https://openalex.org/I1330989302","https://openalex.org/I142606810","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Praveen K. Thallapally","raw_affiliation_strings":["Pacific Northwest National Laboratory, Richland, Washington 99354, United States"],"affiliations":[{"raw_affiliation_string":"Pacific Northwest National Laboratory, Richland, Washington 99354, United States","institution_ids":["https://openalex.org/I142606810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064053803","display_name":"Xiaoli Z. Fern","orcid":null},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoli Z. Fern","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon 97331, United States"],"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon 97331, United States","institution_ids":["https://openalex.org/I131249849"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009640996","display_name":"Cory M. Simon","orcid":"https://orcid.org/0000-0002-8181-9178"},"institutions":[{"id":"https://openalex.org/I131249849","display_name":"Oregon State University","ror":"https://ror.org/00ysfqy60","country_code":"US","type":"education","lineage":["https://openalex.org/I131249849"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Cory M. Simon","raw_affiliation_strings":["School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon 97331, United States"],"affiliations":[{"raw_affiliation_string":"School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon 97331, United States","institution_ids":["https://openalex.org/I131249849"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5009640996"],"corresponding_institution_ids":["https://openalex.org/I131249849"],"apc_list":null,"apc_paid":null,"fwci":0.8988,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.68932671,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"62","issue":"3","first_page":"423","last_page":"432"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10096","display_name":"Metal-Organic Frameworks: Synthesis and Applications","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1604","display_name":"Inorganic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10096","display_name":"Metal-Organic Frameworks: Synthesis and Applications","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1604","display_name":"Inorganic 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/T12038","display_name":"Covalent Organic Framework Applications","score":0.9991999864578247,"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/T10995","display_name":"Methane Hydrates and Related Phenomena","score":0.9926000237464905,"subfield":{"id":"https://openalex.org/subfields/2304","display_name":"Environmental Chemistry"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.8225324153900146},{"id":"https://openalex.org/keywords/crystal-structure","display_name":"Crystal structure","score":0.5108956694602966},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4054873585700989},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.34490418434143066},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.32028523087501526},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.21705570816993713},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12371516227722168}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.8225324153900146},{"id":"https://openalex.org/C115624301","wikidata":"https://www.wikidata.org/wiki/Q895901","display_name":"Crystal structure","level":2,"score":0.5108956694602966},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4054873585700989},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.34490418434143066},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32028523087501526},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.21705570816993713},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12371516227722168},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000073396","descriptor_name":"Metal-Organic Frameworks","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000073396","descriptor_name":"Metal-Organic Frameworks","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000073396","descriptor_name":"Metal-Organic Frameworks","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016062","descriptor_name":"Porosity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016062","descriptor_name":"Porosity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016062","descriptor_name":"Porosity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.1c01219","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c01219","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:35029112","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35029112","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":[{"id":"https://openalex.org/G7748190160","display_name":null,"funder_award_id":"1920945","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G906743308","display_name":null,"funder_award_id":"HDTRA-19-31270","funder_id":"https://openalex.org/F4320332186","funder_display_name":"Defense Threat Reduction Agency"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332186","display_name":"Defense Threat Reduction Agency","ror":"https://ror.org/04tz64554"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":85,"referenced_works":["https://openalex.org/W1677747913","https://openalex.org/W1943588217","https://openalex.org/W1963883777","https://openalex.org/W1967019083","https://openalex.org/W1968896148","https://openalex.org/W1979533634","https://openalex.org/W1980745570","https://openalex.org/W1982870104","https://openalex.org/W1992764450","https://openalex.org/W2018608055","https://openalex.org/W2028046413","https://openalex.org/W2031390939","https://openalex.org/W2057069782","https://openalex.org/W2071227523","https://openalex.org/W2072170322","https://openalex.org/W2090752769","https://openalex.org/W2091161882","https://openalex.org/W2100716186","https://openalex.org/W2102913801","https://openalex.org/W2105761150","https://openalex.org/W2120575449","https://openalex.org/W2121237359","https://openalex.org/W2126359798","https://openalex.org/W2138085558","https://openalex.org/W2141939342","https://openalex.org/W2168843969","https://openalex.org/W2241555812","https://openalex.org/W2304767338","https://openalex.org/W2317224917","https://openalex.org/W2330295469","https://openalex.org/W2335274251","https://openalex.org/W2402426102","https://openalex.org/W2464735106","https://openalex.org/W2474258807","https://openalex.org/W2518763931","https://openalex.org/W2530805533","https://openalex.org/W2554191423","https://openalex.org/W2593730372","https://openalex.org/W2594238106","https://openalex.org/W2599075544","https://openalex.org/W2611292439","https://openalex.org/W2644617594","https://openalex.org/W2756103189","https://openalex.org/W2756398738","https://openalex.org/W2767992952","https://openalex.org/W2769954071","https://openalex.org/W2774131705","https://openalex.org/W2778855703","https://openalex.org/W2789949436","https://openalex.org/W2794728674","https://openalex.org/W2894558355","https://openalex.org/W2915481056","https://openalex.org/W2923018238","https://openalex.org/W2954184206","https://openalex.org/W2954591269","https://openalex.org/W2965068418","https://openalex.org/W2965318963","https://openalex.org/W2969079402","https://openalex.org/W2970315737","https://openalex.org/W2973153050","https://openalex.org/W2983138899","https://openalex.org/W2992843173","https://openalex.org/W3014055873","https://openalex.org/W3016327953","https://openalex.org/W3017210340","https://openalex.org/W3018788426","https://openalex.org/W3033784543","https://openalex.org/W3037876848","https://openalex.org/W3039136197","https://openalex.org/W3039136355","https://openalex.org/W3039975092","https://openalex.org/W3046114221","https://openalex.org/W3047156543","https://openalex.org/W3048908832","https://openalex.org/W3080173631","https://openalex.org/W3104794594","https://openalex.org/W3116905955","https://openalex.org/W3160662705","https://openalex.org/W3163360581","https://openalex.org/W3179113086","https://openalex.org/W3196779934","https://openalex.org/W3197865263","https://openalex.org/W3198276978","https://openalex.org/W3211684172","https://openalex.org/W6601357718"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"PoreMatMod.jl":[0,23,81,112,145],"is":[1,82],"a":[2,26,53,64,68,103],"free,":[3],"open-source,":[4],"user-friendly,":[5],"and":[6,56,123,136],"documented":[7],"Julia":[8],"package":[9],"for":[10,39,75,89,154],"modifying":[11],"crystal":[12,30,43,73,115],"structure":[13,44,74,116,128],"models":[14,117],"of":[15,41,52,71,80,86,102,111,126],"porous":[16],"materials":[17],"such":[18],"as":[19,25],"metal-organic":[20],"frameworks":[21],"(MOFs).":[22],"functions":[24],"find-and-replace":[27,141],"algorithm":[28,36,61],"on":[29,99],"structures":[31,88],"by":[32,144],"leveraging":[33],"(i)":[34],"Ullmann's":[35],"to":[37,49,62,83,113,150],"search":[38],"subgraphs":[40],"the":[42,50,58,72,100],"graph":[45,51],"that":[46],"are":[47],"isomorphic":[48],"query":[54],"fragment":[55,66],"(ii)":[57],"orthogonal":[59],"Procrustes":[60],"align":[63],"replacement":[65],"with":[67,121],"targeted":[69],"substructure":[70],"installation.":[76],"The":[77,140],"prominent":[78],"application":[79],"generate":[84],"libraries":[85],"hypothetical":[87],"virtual":[90],"screenings.":[91],"For":[92],"example,":[93],"one":[94],"can":[95,146],"install":[96],"functional":[97],"groups":[98],"linkers":[101],"parent":[104],"MOF,":[105],"mimicking":[106],"postsynthetic":[107],"modification.":[108],"Other":[109],"applications":[110],"modify":[114],"include":[118],"introducing":[119],"defects":[120],"precision":[122],"correcting":[124],"artifacts":[125],"X-ray":[127],"determination":[129],"(adding":[130],"missing":[131],"hydrogen":[132],"atoms,":[133],"resolving":[134],"disorder,":[135],"removing":[137],"guest":[138],"molecules).":[139],"operations":[142],"implemented":[143],"be":[147],"applied":[148],"broadly":[149],"diverse":[151],"atomistic":[152],"systems":[153],"various":[155],"<i>in":[156],"silico</i>":[157],"structural":[158],"modification":[159],"tasks.":[160]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2}],"updated_date":"2025-11-20T23:13:51.555489","created_date":"2022-04-03T00:00:00"}
