{"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/I165143802","display_name":"The 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"]}],"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/I165143802","display_name":"The 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"]}],"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/I165143802","display_name":"The 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"]}],"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/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/I165143802","display_name":"The 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"]}],"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","Research School of Chemistry, The Australian National University, Canberra, Australian Capital Territory 2601, Australia","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":"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":"Research School of Chemistry, The Australian National University, Canberra, Australian Capital Territory 2601, Australia","institution_ids":["https://openalex.org/I118347636"]},{"raw_affiliation_string":"Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland 4067, Australia","institution_ids":["https://openalex.org/I165143802"]}]}],"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":2.301,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.86816141,"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":[{"id":"https://openalex.org/G20501119","display_name":null,"funder_award_id":"DP180103573","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"}],"funders":[{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"}],"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":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}