{"id":"https://openalex.org/W2945218994","doi":"https://doi.org/10.1021/acs.jcim.9b00269","title":"PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein\u2013Lipid-Bilayer System Building","display_name":"PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein\u2013Lipid-Bilayer System Building","publication_year":2019,"publication_date":"2019-05-23","ids":{"openalex":"https://openalex.org/W2945218994","doi":"https://doi.org/10.1021/acs.jcim.9b00269","mag":"2945218994","pmid":"https://pubmed.ncbi.nlm.nih.gov/31120747"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00269","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00269","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/A5062135666","display_name":"Stephan Schott\u2010Verdugo","orcid":"https://orcid.org/0000-0003-0735-1404"},"institutions":[{"id":"https://openalex.org/I134695357","display_name":"University of Talca","ror":"https://ror.org/01s4gpq44","country_code":"CL","type":"education","lineage":["https://openalex.org/I134695357"]},{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["CL","DE"],"is_corresponding":false,"raw_author_name":"Stephan Schott-Verdugo","raw_affiliation_strings":["Centro de Bioinform\u00e1tica y Simulaci\u00f3n Molecular (CBSM), Faculty of Engineering, Universidad de Talca, 1 Poniente 1141, Casilla 721, Talca, Chile","Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro de Bioinform\u00e1tica y Simulaci\u00f3n Molecular (CBSM), Faculty of Engineering, Universidad de Talca, 1 Poniente 1141, Casilla 721, Talca, Chile","institution_ids":["https://openalex.org/I134695357"]},{"raw_affiliation_string":"Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063949219","display_name":"Holger Gohlke","orcid":"https://orcid.org/0000-0001-8613-1447"},"institutions":[{"id":"https://openalex.org/I171892758","display_name":"Forschungszentrum J\u00fclich","ror":"https://ror.org/02nv7yv05","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I171892758"]},{"id":"https://openalex.org/I4210113364","display_name":"John von Neumann Institute for Computing","ror":"https://ror.org/02zmk8084","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I1305996414","https://openalex.org/I1305996414","https://openalex.org/I169556180","https://openalex.org/I171892758","https://openalex.org/I2801876189","https://openalex.org/I4210113364"]},{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Holger Gohlke","raw_affiliation_strings":["Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany","John von Neumann Institute for Computing (NIC), J\u00fclich Supercomputing Centre (JSC) & Institute for Complex Systems\u2014Structural Biochemistry (ICS 6), Forschungszentrum J\u00fclich GmbH, 52425 J\u00fclich, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8613-1447","affiliations":[{"raw_affiliation_string":"Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"John von Neumann Institute for Computing (NIC), J\u00fclich Supercomputing Centre (JSC) & Institute for Complex Systems\u2014Structural Biochemistry (ICS 6), Forschungszentrum J\u00fclich GmbH, 52425 J\u00fclich, Germany","institution_ids":["https://openalex.org/I4210113364","https://openalex.org/I171892758"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5063949219"],"corresponding_institution_ids":["https://openalex.org/I171892758","https://openalex.org/I4210113364","https://openalex.org/I44260953"],"apc_list":null,"apc_paid":null,"fwci":6.8388,"has_fulltext":false,"cited_by_count":251,"citation_normalized_percentile":{"value":0.97797144,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"59","issue":"6","first_page":"2522","last_page":"2528"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9997000098228455,"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/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9997000098228455,"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":0.9961000084877014,"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/T12763","display_name":"ATP Synthase and ATPases Research","score":0.9902999997138977,"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/simple","display_name":"Simple (philosophy)","score":0.789372444152832},{"id":"https://openalex.org/keywords/lipid-bilayer","display_name":"Lipid bilayer","score":0.7064691781997681},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6964982748031616},{"id":"https://openalex.org/keywords/bilayer","display_name":"Bilayer","score":0.5864247679710388},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4648754894733429},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.45485830307006836},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.4284564256668091},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.3313808739185333},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.328909695148468},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.22786474227905273},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1767762005329132},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11618489027023315},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.0837230384349823}],"concepts":[{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.789372444152832},{"id":"https://openalex.org/C39944091","wikidata":"https://www.wikidata.org/wiki/Q423279","display_name":"Lipid bilayer","level":3,"score":0.7064691781997681},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6964982748031616},{"id":"https://openalex.org/C192157962","wikidata":"https://www.wikidata.org/wiki/Q4087243","display_name":"Bilayer","level":3,"score":0.5864247679710388},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4648754894733429},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.45485830307006836},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.4284564256668091},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.3313808739185333},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.328909695148468},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.22786474227905273},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1767762005329132},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11618489027023315},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0837230384349823},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000080943","descriptor_name":"Bacterial Outer Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000080943","descriptor_name":"Bacterial Outer Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000080943","descriptor_name":"Bacterial Outer Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015221","descriptor_name":"Potassium Channels","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015221","descriptor_name":"Potassium Channels","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015221","descriptor_name":"Potassium Channels","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D048170","descriptor_name":"Streptomyces lividans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D048170","descriptor_name":"Streptomyces lividans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D048170","descriptor_name":"Streptomyces lividans","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.9b00269","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00269","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:31120747","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31120747","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":[{"id":"https://metadata.un.org/sdg/9","score":0.49000000953674316,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1953176015","display_name":null,"funder_award_id":"FOR 2518 (GO 1367/2-1)","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2212661399","display_name":null,"funder_award_id":"267205415 ? SFB 1208","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1560425209","https://openalex.org/W1975027906","https://openalex.org/W1976499671","https://openalex.org/W1980131439","https://openalex.org/W1981225934","https://openalex.org/W1990771438","https://openalex.org/W2003949305","https://openalex.org/W2015111515","https://openalex.org/W2015481485","https://openalex.org/W2025927596","https://openalex.org/W2029088347","https://openalex.org/W2029335938","https://openalex.org/W2029667189","https://openalex.org/W2036260386","https://openalex.org/W2057843068","https://openalex.org/W2059169173","https://openalex.org/W2060872117","https://openalex.org/W2067165323","https://openalex.org/W2067263573","https://openalex.org/W2071475257","https://openalex.org/W2086436538","https://openalex.org/W2110474020","https://openalex.org/W2111138318","https://openalex.org/W2114239896","https://openalex.org/W2115339329","https://openalex.org/W2121727772","https://openalex.org/W2124653618","https://openalex.org/W2143070723","https://openalex.org/W2149378523","https://openalex.org/W2149628585","https://openalex.org/W2156835500","https://openalex.org/W2160679445","https://openalex.org/W2168269595","https://openalex.org/W2206954826","https://openalex.org/W2229781928","https://openalex.org/W2290785648","https://openalex.org/W2314330043","https://openalex.org/W2323104785","https://openalex.org/W2327285702","https://openalex.org/W2334732464","https://openalex.org/W2346941655","https://openalex.org/W2404280981","https://openalex.org/W2564298127","https://openalex.org/W2734926260","https://openalex.org/W2762489564","https://openalex.org/W2905232362"],"related_works":["https://openalex.org/W2389992822","https://openalex.org/W2061481432","https://openalex.org/W2100090167","https://openalex.org/W2718515487","https://openalex.org/W4367601614","https://openalex.org/W2072230736","https://openalex.org/W1963901611","https://openalex.org/W2059795428","https://openalex.org/W4206087209","https://openalex.org/W2289704112"],"abstract_inverted_index":{"We":[0],"present":[1],"PACKMOL-Memgen,":[2],"a":[3,35,38],"simple-to-use,":[4],"generalized":[5],"workflow":[6],"for":[7,86],"automated":[8],"building":[9],"of":[10,31,34],"membrane-protein-lipid-bilayer":[11],"systems":[12,47],"based":[13],"on":[14,75],"open-source":[15],"tools":[16],"including":[17],"Packmol,":[18],"memembed,":[19],"pdbremix,":[20],"and":[21,40,50,73,79],"AmberTools.":[22],"Compared":[23],"with":[24,71],"web-interface-based":[25],"related":[26],"tools,":[27],"PACKMOL-Memgen":[28,68],"allows":[29],"setup":[30],"multiple":[32],"configurations":[33,55],"system":[36],"in":[37,56],"user-friendly":[39],"efficient":[41],"manner":[42],"within":[43],"minutes.":[44],"The":[45],"generated":[46],"are":[48],"well-packed":[49],"thus":[51],"well-suited":[52],"as":[53],"starting":[54],"MD":[57],"simulations":[58],"under":[59],"periodic":[60],"boundary":[61],"conditions,":[62],"requiring":[63],"only":[64],"moderate":[65],"equilibration":[66],"times.":[67],"is":[69],"distributed":[70],"AmberTools":[72],"runs":[74],"most":[76],"computing":[77],"platforms,":[78],"its":[80],"output":[81],"can":[82],"also":[83],"be":[84],"used":[85],"CHARMM":[87],"or":[88],"adapted":[89],"to":[90],"other":[91],"molecular-simulation":[92],"packages.":[93]},"counts_by_year":[{"year":2026,"cited_by_count":19},{"year":2025,"cited_by_count":66},{"year":2024,"cited_by_count":49},{"year":2023,"cited_by_count":37},{"year":2022,"cited_by_count":30},{"year":2021,"cited_by_count":32},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":5}],"updated_date":"2026-06-17T08:01:34.144755","created_date":"2025-10-10T00:00:00"}