{"id":"https://openalex.org/W2001065096","doi":"https://doi.org/10.1186/1758-2946-3-s1-p43","title":"Coarse-grained and all-atom MD simulations with Gromacs based on CELLmicrocosmos 2.2 model membranes","display_name":"Coarse-grained and all-atom MD simulations with Gromacs based on CELLmicrocosmos 2.2 model membranes","publication_year":2011,"publication_date":"2011-04-19","ids":{"openalex":"https://openalex.org/W2001065096","doi":"https://doi.org/10.1186/1758-2946-3-s1-p43","mag":"2001065096"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-3-s1-p43","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p43","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P43","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P43","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059487495","display_name":"Bj\u00f6rn Sommer","orcid":"https://orcid.org/0000-0003-1514-9898"},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"B Sommer","raw_affiliation_strings":["Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany"],"affiliations":[{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]},{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068831397","display_name":"T. Dingersen","orcid":null},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"T Dingersen","raw_affiliation_strings":["Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany"],"affiliations":[{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]},{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110183718","display_name":"C. Gamroth","orcid":null},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"C Gamroth","raw_affiliation_strings":["Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany"],"affiliations":[{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]},{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076440371","display_name":"Andr\u00e9 J. Heissmann","orcid":null},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"AJ Heissmann","raw_affiliation_strings":["Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany"],"affiliations":[{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]},{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004217896","display_name":"Gunther Lukat","orcid":null},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"G Lukat","raw_affiliation_strings":["Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany"],"affiliations":[{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]},{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045477435","display_name":"Ralf Rotzoll","orcid":null},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"R Rotzoll","raw_affiliation_strings":["Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany"],"affiliations":[{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]},{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111382087","display_name":"S. Rubert","orcid":null},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"S Rubert","raw_affiliation_strings":["Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany"],"affiliations":[{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]},{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051126399","display_name":"Alexander Sch\u00e4fer","orcid":"https://orcid.org/0000-0002-4258-0651"},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"A Sch\u00e4fer","raw_affiliation_strings":["Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany"],"affiliations":[{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, 33615, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]},{"raw_affiliation_string":"Bio-/Medical Informatics Department, Bielefeld University, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024793839","display_name":"Jens Kr\u00fcger","orcid":"https://orcid.org/0000-0002-2636-3163"},"institutions":[{"id":"https://openalex.org/I206945453","display_name":"Paderborn University","ror":"https://ror.org/058kzsd48","country_code":"DE","type":"education","lineage":["https://openalex.org/I206945453"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"J Kr\u00fcger","raw_affiliation_strings":["Department of Chemistry, University of Paderborn, 33098, Paderborn, Germany","Department of Chemistry University of Paderborn Paderborn, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Paderborn, 33098, Paderborn, Germany","institution_ids":["https://openalex.org/I206945453"]},{"raw_affiliation_string":"Department of Chemistry University of Paderborn Paderborn, Germany","institution_ids":["https://openalex.org/I206945453"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5059487495"],"corresponding_institution_ids":["https://openalex.org/I20121455"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07817743,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"3","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12029","display_name":"DNA and Biological Computing","score":0.9955000281333923,"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/T12029","display_name":"DNA and Biological Computing","score":0.9955000281333923,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9952999949455261,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9896000027656555,"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/computer-science","display_name":"Computer science","score":0.7012421488761902},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6595422029495239},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.617575466632843},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.6128442883491516},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5545142889022827},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5431044101715088},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.48942533135414124},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.47288861870765686},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.28892892599105835},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2644197642803192},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.18509697914123535},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.17397525906562805},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.08996811509132385}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7012421488761902},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6595422029495239},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.617575466632843},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.6128442883491516},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5545142889022827},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5431044101715088},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.48942533135414124},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.47288861870765686},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.28892892599105835},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2644197642803192},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.18509697914123535},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.17397525906562805},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.08996811509132385},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/1758-2946-3-s1-p43","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p43","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P43","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2091980","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3083600","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-3-s1-p43","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p43","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P43","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2001065096.pdf","grobid_xml":"https://content.openalex.org/works/W2001065096.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W1966078827","https://openalex.org/W1980406693","https://openalex.org/W2130479394"],"related_works":["https://openalex.org/W2090630809","https://openalex.org/W2153650863","https://openalex.org/W4246050813","https://openalex.org/W4253991465","https://openalex.org/W2298319713","https://openalex.org/W4387804157","https://openalex.org/W3207853523","https://openalex.org/W3168273531","https://openalex.org/W2589205199","https://openalex.org/W2088034942"],"abstract_inverted_index":{"The":[0,18,112,140],"CELLmicrocosmos":[1],"MembraneEditor":[2],"(CmME)":[3],"[1]":[4],"enables":[5],"researchers":[6],"to":[7,58,131],"generate":[8],"PDB":[9],"[2]":[10],"based":[11,182,199],"membrane":[12,145],"structures":[13,122],"in":[14],"a":[15,61,98,180],"convenient":[16],"way.":[17],"lipid":[19,171,177],"distribution":[20],"is":[21,41,115,188],"computed":[22],"by":[23,117],"algorithms":[24],"working":[25],"on":[26,183],"the":[27,31,36,45,71,84,89,102,136,159,168,184,192],"outer":[28],"shapes":[29],"of":[30,48,86,101,105,135,161,170,176,195],"molecules.":[32],"For":[33],"this":[34,68],"reason,":[35],"computation":[37,175],"and":[38,75,93,120,129,173,197],"visualization":[39],"process":[40],"very":[42],"fast,":[43],"while":[44],"atomistic":[46],"structure":[47],"each":[49],"single":[50],"molecule":[51],"remains":[52],"unchanged.\r\n\r\nPDB":[53],"membranes":[54,87],"can":[55],"be":[56],"exported":[57],"Gromacs":[59,76,128,198],"[3],":[60],"molecular":[62],"dynamic":[63],"simulation":[64,85],"(MD)":[65],"program.":[66],"In":[67],"new":[69],"approach":[70],"workflow":[72],"between":[73],"CmME":[74,137,185,196],"has":[77,109],"been":[78,110],"improved.":[79],"Two":[80],"major":[81],"strategies":[82],"for":[83],"are":[88],"all":[90],"atom":[91],"(AA)":[92],"coarse-grained":[94,107],"(CG)":[95],"approach.":[96],"As":[97],"logical":[99],"consequence":[100],"shape-based":[103],"principle":[104],"CmME,":[106,125],"support":[108],"implemented.":[111],"ongoing":[113],"work":[114],"presented":[116],"comparing":[118],"AA":[119],"CG":[121,162],"generated":[123],"with":[124,127],"simulated":[126],"reverse-parsed":[130],"CmME.\r\n\r\nNewly":[132],"implemented":[133],"features":[134],"MD":[138],"Edition:\r\n\r\n\u2022":[139],"Membrane":[141],"Shifter":[142],"Tool,":[143],"enabling":[144],"model":[146],"repositioning\r\n\r\n\u2022":[147],"Shape":[148],"generation":[149],"taking":[150],"periodic":[151],"boundaries":[152],"into":[153],"account\r\n\r\n\u2022":[154],"A":[155],"Molecule":[156],"Editor,":[157],"supporting":[158],"definition":[160],"particles\r\n\r\n\u2022":[163],"Advanced":[164],"raft":[165],"support,":[166],"allowing":[167,191],"analysis":[169],"values":[172],"raft-restricted":[174],"distributions.\r\n\r\nIn":[178],"addition,":[179],"GUI":[181],"algorithm":[186],"interface":[187],"being":[189],"implemented,":[190],"comfortable":[193],"handling":[194],"workflows.":[200]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
