{"id":"https://openalex.org/W4408514545","doi":"https://doi.org/10.1021/acs.jcim.4c02375","title":"<i>PolyConstruct</i>: Adapting Biomolecular Simulation Pipelines for Polymers with <i>PolyBuild</i>, <i>PolyConf</i>, and <i>PolyTop</i>","display_name":"<i>PolyConstruct</i>: Adapting Biomolecular Simulation Pipelines for Polymers with <i>PolyBuild</i>, <i>PolyConf</i>, and <i>PolyTop</i>","publication_year":2025,"publication_date":"2025-03-17","ids":{"openalex":"https://openalex.org/W4408514545","doi":"https://doi.org/10.1021/acs.jcim.4c02375","pmid":"https://pubmed.ncbi.nlm.nih.gov/40097192"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c02375","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02375","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/A5075942321","display_name":"Rangika Munaweera","orcid":"https://orcid.org/0000-0001-9675-7662"},"institutions":[{"id":"https://openalex.org/I4210113188","display_name":"Institute of Bioengineering and Nanotechnology","ror":"https://ror.org/022xyn875","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210113188"]},{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU","SG"],"is_corresponding":false,"raw_author_name":"Rangika Munaweera","raw_affiliation_strings":["Australian Institute for Bioengineering and Nanotechnology","University of Queensland","Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland 4067, Australia"],"affiliations":[{"raw_affiliation_string":"Australian Institute for Bioengineering and Nanotechnology","institution_ids":["https://openalex.org/I4210113188"]},{"raw_affiliation_string":"University of Queensland","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland 4067, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062638453","display_name":"Ada Quinn","orcid":"https://orcid.org/0009-0003-1862-0750"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]},{"id":"https://openalex.org/I4210113188","display_name":"Institute of Bioengineering and Nanotechnology","ror":"https://ror.org/022xyn875","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210113188"]},{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU","SG"],"is_corresponding":false,"raw_author_name":"Ada Quinn","raw_affiliation_strings":["Australian Institute for Bioengineering and Nanotechnology","Research School of Chemistry","The Australian National University","University of Queensland","Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland 4067, Australia","Research School of Chemistry, The Australian National University, Canberra, Australian Capital Territory 2601, Australia"],"affiliations":[{"raw_affiliation_string":"Australian Institute for Bioengineering and Nanotechnology","institution_ids":["https://openalex.org/I4210113188"]},{"raw_affiliation_string":"Research School of Chemistry","institution_ids":[]},{"raw_affiliation_string":"The Australian National University","institution_ids":["https://openalex.org/I118347636"]},{"raw_affiliation_string":"University of Queensland","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland 4067, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Research School of Chemistry, The Australian National University, Canberra, Australian Capital Territory 2601, Australia","institution_ids":["https://openalex.org/I118347636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116654923","display_name":"Luna Morrow","orcid":null},"institutions":[{"id":"https://openalex.org/I4210113188","display_name":"Institute of Bioengineering and Nanotechnology","ror":"https://ror.org/022xyn875","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210113188"]},{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]}],"countries":["AU","SG"],"is_corresponding":false,"raw_author_name":"Luna Morrow","raw_affiliation_strings":["Australian Institute for Bioengineering and Nanotechnology","University of Queensland","Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland 4067, Australia"],"affiliations":[{"raw_affiliation_string":"Australian Institute for Bioengineering and Nanotechnology","institution_ids":["https://openalex.org/I4210113188"]},{"raw_affiliation_string":"University of Queensland","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland 4067, Australia","institution_ids":["https://openalex.org/I165143802"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075900916","display_name":"Richard A. Morris","orcid":"https://orcid.org/0000-0002-0149-153X"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Richard A. Morris","raw_affiliation_strings":["Research School of Chemistry","The Australian National University","Research School of Chemistry, The Australian National University, Canberra, Australian Capital Territory 2601, Australia"],"affiliations":[{"raw_affiliation_string":"Research School of Chemistry","institution_ids":[]},{"raw_affiliation_string":"The Australian National University","institution_ids":["https://openalex.org/I118347636"]},{"raw_affiliation_string":"Research School of Chemistry, The Australian National University, Canberra, Australian Capital Territory 2601, Australia","institution_ids":["https://openalex.org/I118347636"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075731186","display_name":"Megan L. O\u2019Mara","orcid":"https://orcid.org/0000-0002-8764-1585"},"institutions":[{"id":"https://openalex.org/I165143802","display_name":"University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I4210113188","display_name":"Institute of Bioengineering and Nanotechnology","ror":"https://ror.org/022xyn875","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210113188"]},{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU","SG"],"is_corresponding":true,"raw_author_name":"Megan L. O\u2019Mara","raw_affiliation_strings":["Australian Institute for Bioengineering and Nanotechnology","Research School of Chemistry","The Australian National University","University of Queensland","Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland 4067, Australia","Research School of Chemistry, The Australian National University, Canberra, Australian Capital Territory 2601, Australia"],"affiliations":[{"raw_affiliation_string":"Australian Institute for Bioengineering and Nanotechnology","institution_ids":["https://openalex.org/I4210113188"]},{"raw_affiliation_string":"Research School of Chemistry","institution_ids":[]},{"raw_affiliation_string":"The Australian National University","institution_ids":["https://openalex.org/I118347636"]},{"raw_affiliation_string":"University of Queensland","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland 4067, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Research School of Chemistry, The Australian National University, Canberra, Australian Capital Territory 2601, Australia","institution_ids":["https://openalex.org/I118347636"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5075731186"],"corresponding_institution_ids":["https://openalex.org/I118347636","https://openalex.org/I165143802","https://openalex.org/I4210113188"],"apc_list":null,"apc_paid":null,"fwci":2.5694,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.88119607,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"65","issue":"10","first_page":"4918","last_page":"4931"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9811999797821045,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9811999797821045,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9276000261306763,"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/polymer","display_name":"Polymer","score":0.4011758863925934},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.28527140617370605},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.11003303527832031}],"concepts":[{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.4011758863925934},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.28527140617370605},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.11003303527832031}],"mesh":[{"descriptor_ui":"D011108","descriptor_name":"Polymers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011108","descriptor_name":"Polymers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c02375","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02375","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:40097192","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40097192","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":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1491824558","https://openalex.org/W1995816895","https://openalex.org/W2003094937","https://openalex.org/W2015688756","https://openalex.org/W2019693219","https://openalex.org/W2028046413","https://openalex.org/W2032592607","https://openalex.org/W2035266068","https://openalex.org/W2035687084","https://openalex.org/W2037788435","https://openalex.org/W2055793978","https://openalex.org/W2057477511","https://openalex.org/W2062457450","https://openalex.org/W2067174909","https://openalex.org/W2070753604","https://openalex.org/W2086946786","https://openalex.org/W2092408620","https://openalex.org/W2097888262","https://openalex.org/W2103945336","https://openalex.org/W2118233996","https://openalex.org/W2119267663","https://openalex.org/W2128572087","https://openalex.org/W2132629607","https://openalex.org/W2137042757","https://openalex.org/W2169678694","https://openalex.org/W2170711116","https://openalex.org/W2222589778","https://openalex.org/W2292781229","https://openalex.org/W2296487627","https://openalex.org/W2420659973","https://openalex.org/W2510475640","https://openalex.org/W2540491215","https://openalex.org/W2555870966","https://openalex.org/W2590260721","https://openalex.org/W2606142660","https://openalex.org/W2751955879","https://openalex.org/W2894227923","https://openalex.org/W2894639568","https://openalex.org/W2910009329","https://openalex.org/W2912807874","https://openalex.org/W2918249593","https://openalex.org/W2922897908","https://openalex.org/W2943856066","https://openalex.org/W2949223833","https://openalex.org/W2965868169","https://openalex.org/W2996232687","https://openalex.org/W3035762603","https://openalex.org/W3046751266","https://openalex.org/W3092054218","https://openalex.org/W3145808230","https://openalex.org/W3146814598","https://openalex.org/W3173810198","https://openalex.org/W3203050184","https://openalex.org/W4205573868","https://openalex.org/W4213193244","https://openalex.org/W4225515600","https://openalex.org/W4285589268","https://openalex.org/W4303981447","https://openalex.org/W4308586705","https://openalex.org/W4313839728","https://openalex.org/W4317433346","https://openalex.org/W4319211574","https://openalex.org/W4380422299","https://openalex.org/W4385519663","https://openalex.org/W4386836991","https://openalex.org/W4387300481","https://openalex.org/W4387440676","https://openalex.org/W4388879624","https://openalex.org/W4395068993","https://openalex.org/W4400723012","https://openalex.org/W4403466652","https://openalex.org/W4407749149"],"related_works":["https://openalex.org/W623819857","https://openalex.org/W579750849","https://openalex.org/W1972967867","https://openalex.org/W4388376352","https://openalex.org/W4254338972","https://openalex.org/W3103565007","https://openalex.org/W2359352034","https://openalex.org/W4309200630","https://openalex.org/W587830988","https://openalex.org/W2341987222"],"abstract_inverted_index":{"Molecular":[0],"dynamics":[1,28],"simulations":[2,29,44,71],"are":[3],"invaluable":[4],"tools":[5],"that":[6,39,59],"provide":[7],"both":[8],"a":[9,13,34,55],"molecular":[10,27],"understanding":[11],"and":[12,36,49,74,83,94,101,107,112,120],"means":[14],"for":[15,45,66,85,97],"the":[16,31,41,61,105],"rational":[17],"design":[18],"of":[19,33,43,72,109,116],"polymers.":[20,76,122],"A":[21],"key":[22],"bottleneck":[23],"in":[24],"current":[25],"polymer":[26,47,99],"is":[30],"lack":[32],"comprehensive":[35],"generalizable":[37,56],"method":[38],"streamlines":[40],"preparation":[42],"novel":[46],"architectures":[48,100],"chemistries.":[50,102],"Here,":[51],"we":[52],"present":[53],"<i>PolyConstruct</i>,":[54],"computational":[57],"framework":[58],"leverages":[60],"GROMACS":[62],"biomolecular":[63],"simulation":[64],"package":[65],"force":[67],"field":[68],"agnostic":[69],"atomistic":[70],"biocompatible":[73],"stimuli-responsive":[75],"<i>PolyConstruct</i>":[77],"contains":[78],"three":[79],"workflows,":[80],"<i>PolyBuild</i>,":[81,110],"<i>PolyTop</i>,":[82,111],"<i>PolyConf</i>,":[84],"generating":[86],"chemically":[87],"accurate":[88],"topology":[89],"parameters":[90,93],"from":[91],"monomer":[92],"structural":[95],"coordinates":[96],"complex":[98],"We":[103],"highlight":[104],"utility":[106],"robustness":[108],"<i>PolyConf</i>":[113],"with":[114],"examples":[115],"linear,":[117],"branched,":[118],"star,":[119],"dendritic":[121]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2025-12-22T23:10:17.713674","created_date":"2025-10-10T00:00:00"}
