{"id":"https://openalex.org/W1993149340","doi":"https://doi.org/10.1021/ci3000453","title":"LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations","display_name":"LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations","publication_year":2012,"publication_date":"2012-09-18","ids":{"openalex":"https://openalex.org/W1993149340","doi":"https://doi.org/10.1021/ci3000453","mag":"1993149340","pmid":"https://pubmed.ncbi.nlm.nih.gov/22989154"},"language":"en","primary_location":{"id":"doi:10.1021/ci3000453","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci3000453","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/A5028974311","display_name":"Thomas Schmidt","orcid":"https://orcid.org/0000-0001-8116-7555"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Thomas H. Schmidt","raw_affiliation_strings":["Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences (LIMES) Institute, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences (LIMES) Institute, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025197741","display_name":"Christian Kandt","orcid":null},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christian Kandt","raw_affiliation_strings":["Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences (LIMES) Institute, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Structural Biology, Department of Life Science Informatics B-IT, Life & Medical Sciences (LIMES) Institute, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5028974311"],"corresponding_institution_ids":["https://openalex.org/I135140700"],"apc_list":null,"apc_paid":null,"fwci":4.3341,"has_fulltext":false,"cited_by_count":125,"citation_normalized_percentile":{"value":0.95259059,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"52","issue":"10","first_page":"2657","last_page":"2669"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9952999949455261,"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"}},"topics":[{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","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/T10044","display_name":"Protein Structure and Dynamics","score":0.992900013923645,"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":0.9815999865531921,"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/membrane","display_name":"Membrane","score":0.6272091865539551},{"id":"https://openalex.org/keywords/membrane-protein","display_name":"Membrane protein","score":0.5675850510597229},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.5497111678123474},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5252325534820557},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5217055678367615},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5109280943870544},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.47902408242225647},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.47412919998168945},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.47392043471336365},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4289149045944214},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.40137016773223877},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3904626965522766},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.33815908432006836},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.181365966796875},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1745370626449585},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13553977012634277},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.11521148681640625},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.10898289084434509},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10327020287513733}],"concepts":[{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.6272091865539551},{"id":"https://openalex.org/C144647389","wikidata":"https://www.wikidata.org/wiki/Q423042","display_name":"Membrane protein","level":3,"score":0.5675850510597229},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.5497111678123474},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5252325534820557},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5217055678367615},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5109280943870544},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.47902408242225647},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.47412919998168945},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.47392043471336365},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4289149045944214},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.40137016773223877},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3904626965522766},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33815908432006836},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.181365966796875},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1745370626449585},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13553977012634277},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.11521148681640625},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.10898289084434509},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10327020287513733},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":null,"qualifier_name":null,"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":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010743","descriptor_name":"Phospholipids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010743","descriptor_name":"Phospholipids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010743","descriptor_name":"Phospholipids","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci3000453","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci3000453","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:22989154","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22989154","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":[{"score":0.6499999761581421,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1493069182","https://openalex.org/W1892148740","https://openalex.org/W1966078827","https://openalex.org/W1975304761","https://openalex.org/W1977569471","https://openalex.org/W1982338804","https://openalex.org/W1985400607","https://openalex.org/W1993236717","https://openalex.org/W1994340275","https://openalex.org/W1996478334","https://openalex.org/W2007176314","https://openalex.org/W2009069785","https://openalex.org/W2011486797","https://openalex.org/W2022993040","https://openalex.org/W2026582002","https://openalex.org/W2026907061","https://openalex.org/W2030683115","https://openalex.org/W2032226429","https://openalex.org/W2035939859","https://openalex.org/W2036847375","https://openalex.org/W2037831301","https://openalex.org/W2038302435","https://openalex.org/W2049562138","https://openalex.org/W2051980410","https://openalex.org/W2053427132","https://openalex.org/W2057972192","https://openalex.org/W2059382484","https://openalex.org/W2060079863","https://openalex.org/W2061804805","https://openalex.org/W2062999231","https://openalex.org/W2069290381","https://openalex.org/W2071571442","https://openalex.org/W2073560270","https://openalex.org/W2075789879","https://openalex.org/W2078126071","https://openalex.org/W2080985792","https://openalex.org/W2094957305","https://openalex.org/W2097775366","https://openalex.org/W2113789703","https://openalex.org/W2116493166","https://openalex.org/W2118940870","https://openalex.org/W2129838159","https://openalex.org/W2132262459","https://openalex.org/W2134762386","https://openalex.org/W2144791518","https://openalex.org/W2145020089","https://openalex.org/W2148395120","https://openalex.org/W2150981663","https://openalex.org/W2158253179","https://openalex.org/W2160947340","https://openalex.org/W2162166182","https://openalex.org/W2168269595","https://openalex.org/W2169980354","https://openalex.org/W2170743627","https://openalex.org/W2396490986","https://openalex.org/W2513885104","https://openalex.org/W2884849918","https://openalex.org/W3012535303","https://openalex.org/W4249100034"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2081900870","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W4255934811","https://openalex.org/W2465382974","https://openalex.org/W2010229520"],"abstract_inverted_index":{"At":[0],"the":[1,10,19,30,33,56,69,108,112,119,122,127,139,143,154,162,166,206,233,281],"beginning":[2],"of":[3,12,22,55,126,138,145,157,179,205,236,274,283,295],"each":[4],"molecular":[5],"dynamics":[6],"membrane":[7,24,46,98,208,293],"simulation":[8],"stands":[9],"generation":[11],"a":[13,52,61,103,149,177,200,265,271],"suitable":[14],"starting":[15],"structure":[16,209],"which":[17,68],"includes":[18],"working":[20],"steps":[21,175],"aligning":[23],"and":[25,27,40,72,80,94,130,168,172,185,194,215,228,277,298],"protein":[26,31,79,129,167],"seamlessly":[28],"accommodating":[29],"in":[32,148,219,256,262],"membrane.":[34,81,131],"Here":[35],"we":[36,286],"introduce":[37],"two":[38],"efficient":[39],"complementary":[41],"methods":[42],"based":[43,66,160],"on":[44,67,102,161],"pre-equilibrated":[45],"patches,":[47],"automating":[48],"these":[49],"steps.":[50],"Using":[51],"voxel-based":[53],"cast":[54],"coarse-grained":[57],"protein,":[58],"LAMBADA":[59,87,106],"computes":[60],"hydrophilicity":[62],"profile-derived":[63],"scoring":[64],"function":[65],"optimal":[70,191],"rotation":[71],"translation":[73],"operations":[74],"are":[75],"determined":[76],"to":[77,176,199,213],"align":[78],"Employing":[82],"an":[83,136],"entirely":[84],"geometrical":[85],"approach,":[86],"is":[88,107,135],"independent":[89],"from":[90],"any":[91],"precalculated":[92],"data":[93],"aligns":[95],"even":[96],"large":[97],"proteins":[99,246,294],"within":[100],"minutes":[101],"regular":[104],"workstation.":[105],"first":[109],"tool":[110,134],"performing":[111],"entire":[113],"alignment":[114],"process":[115],"automatically":[116,183],"while":[117,269],"providing":[118],"user":[120],"with":[121,258],"explicit":[123],"3D":[124],"coordinates":[125],"aligned":[128],"The":[132],"second":[133],"extension":[137],"InflateGRO":[140],"method":[141],"addressing":[142],"shortcomings":[144],"its":[146],"predecessor":[147],"fully":[150,266],"automated":[151,267],"workflow.":[152],"Determining":[153],"exact":[155],"number":[156],"overlapping":[158],"lipids":[159,181],"area":[163],"occupied":[164],"by":[165],"restricting":[169],"expansion,":[170],"compression":[171],"energy":[173],"minimization":[174],"subset":[178],"relevant":[180],"through":[182],"calculated":[184],"system-optimized":[186],"operation":[187],"parameters,":[188],"InflateGRO2":[189,222],"yields":[190],"lipid":[192,196,240],"packing":[193],"reduces":[195],"vacuum":[197],"exposure":[198],"minimum":[201],"preserving":[202],"as":[203,210,242,244],"much":[204],"equilibrated":[207],"possible.":[211],"Applicable":[212],"atomistic":[214],"coarse":[216],"grain":[217],"structures":[218],"MARTINI":[220],"format,":[221],"offers":[223],"high":[224],"accuracy,":[225],"fast":[226],"performance,":[227],"increased":[229],"application":[230],"flexibility":[231],"permitting":[232,264],"easy":[234],"preparation":[235],"systems":[237],"exhibiting":[238],"heterogeneous":[239],"composition":[241],"well":[243],"embedding":[245],"into":[247],"multiple":[248],"membranes.":[249],"Both":[250],"tools":[251],"can":[252],"be":[253],"used":[254],"separately,":[255],"combination":[257],"other":[259],"methods,":[260,285],"or":[261],"tandem":[263],"workflow":[268],"retaining":[270],"maximum":[272],"level":[273],"usage":[275],"control":[276],"flexibility.":[278],"To":[279],"assess":[280],"performance":[282],"both":[284],"carried":[287],"out":[288],"test":[289],"runs":[290],"using":[291],"22":[292],"different":[296],"size":[297],"transmembrane":[299],"structure.":[300]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":19},{"year":2015,"cited_by_count":17},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":5}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}