{"id":"https://openalex.org/W2539103838","doi":"https://doi.org/10.1021/acs.jcim.6b00350","title":"Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model","display_name":"Coarse-Grained Simulations of Membrane Insertion and Folding of Small Helical Proteins Using the CABS Model","publication_year":2016,"publication_date":"2016-10-24","ids":{"openalex":"https://openalex.org/W2539103838","doi":"https://doi.org/10.1021/acs.jcim.6b00350","mag":"2539103838"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00350","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00350","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"],"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/A5002422109","display_name":"Wojciech Pu\u0142awski","orcid":"https://orcid.org/0000-0002-4837-1148"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Wojciech Pulawski","raw_affiliation_strings":["Faculty\rof Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"Faculty\rof Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080226074","display_name":"Micha\u0142 H. Jamr\u00f3z","orcid":"https://orcid.org/0000-0002-7255-6476"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Michal Jamroz","raw_affiliation_strings":["Faculty\rof Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"Faculty\rof Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035862091","display_name":"Micha\u0142 Koli\u0144ski","orcid":"https://orcid.org/0000-0003-1047-2186"},"institutions":[{"id":"https://openalex.org/I4210157213","display_name":"Mossakowski Medical Research Institute,  Polish Academy of Sciences","ror":"https://ror.org/05d3ntb42","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210157213","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"funder","lineage":["https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Michal Kolinski","raw_affiliation_strings":["Bioinformatics\rLaboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"Bioinformatics\rLaboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland","institution_ids":["https://openalex.org/I4210157213","https://openalex.org/I99542240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025085688","display_name":"Andrzej Koli\u0144ski","orcid":"https://orcid.org/0000-0002-8830-2315"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Andrzej Kolinski","raw_affiliation_strings":["Faculty\rof Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"Faculty\rof Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006850152","display_name":"Sebastian Kmiecik","orcid":"https://orcid.org/0000-0001-7623-0935"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Sebastian Kmiecik","raw_affiliation_strings":["Faculty\rof Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland"],"affiliations":[{"raw_affiliation_string":"Faculty\rof Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5002422109"],"corresponding_institution_ids":["https://openalex.org/I4654613"],"apc_list":null,"apc_paid":null,"fwci":2.1675,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.87868664,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"56","issue":"11","first_page":"2207","last_page":"2215"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9994999766349792,"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":0.9984999895095825,"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/folding","display_name":"Folding (DSP implementation)","score":0.6613626480102539},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.6441980004310608},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5815771818161011},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5752024054527283},{"id":"https://openalex.org/keywords/membrane-protein","display_name":"Membrane protein","score":0.5692973732948303},{"id":"https://openalex.org/keywords/globular-protein","display_name":"Globular protein","score":0.5482611060142517},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.5155348777770996},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.4754466712474823},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4717603325843811},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43948161602020264},{"id":"https://openalex.org/keywords/model-system","display_name":"Model system","score":0.4278402328491211},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4194800555706024},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.39894670248031616},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.2542669475078583},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16459670662879944},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.141649067401886},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1371287703514099},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12370079755783081},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11932739615440369}],"concepts":[{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.6613626480102539},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.6441980004310608},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5815771818161011},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5752024054527283},{"id":"https://openalex.org/C144647389","wikidata":"https://www.wikidata.org/wiki/Q423042","display_name":"Membrane protein","level":3,"score":0.5692973732948303},{"id":"https://openalex.org/C105168689","wikidata":"https://www.wikidata.org/wiki/Q901969","display_name":"Globular protein","level":2,"score":0.5482611060142517},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5155348777770996},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4754466712474823},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4717603325843811},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43948161602020264},{"id":"https://openalex.org/C2988540567","wikidata":"https://www.wikidata.org/wiki/Q12070446","display_name":"Model system","level":2,"score":0.4278402328491211},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4194800555706024},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.39894670248031616},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.2542669475078583},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16459670662879944},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.141649067401886},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1371287703514099},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12370079755783081},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11932739615440369},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","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/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1021/acs.jcim.6b00350","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00350","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"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4961122233","display_name":null,"funder_award_id":"TEAM/2011-7/6","funder_id":"https://openalex.org/F4320321042","funder_display_name":"Fundacja na rzecz Nauki Polskiej"},{"id":"https://openalex.org/G6798663048","display_name":null,"funder_award_id":"MAESTRO 2014/14/A/ST6/0008","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"},{"id":"https://openalex.org/G6878478280","display_name":null,"funder_award_id":"2011/01/D/NZ2/05314","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"},{"id":"https://openalex.org/G8427492030","display_name":null,"funder_award_id":"TEAM/2011-7/6","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321042","display_name":"Fundacja na rzecz Nauki Polskiej","ror":"https://ror.org/048zd9m77"},{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W9614526","https://openalex.org/W165214403","https://openalex.org/W1511973158","https://openalex.org/W1527813693","https://openalex.org/W1544009106","https://openalex.org/W1934953004","https://openalex.org/W1938743025","https://openalex.org/W1939843585","https://openalex.org/W1969549030","https://openalex.org/W1971456069","https://openalex.org/W1975304761","https://openalex.org/W1984262246","https://openalex.org/W1987134040","https://openalex.org/W1998835042","https://openalex.org/W1999133834","https://openalex.org/W2006177920","https://openalex.org/W2010631124","https://openalex.org/W2011051106","https://openalex.org/W2021801729","https://openalex.org/W2030388655","https://openalex.org/W2042153675","https://openalex.org/W2044944786","https://openalex.org/W2047022491","https://openalex.org/W2049286183","https://openalex.org/W2051545676","https://openalex.org/W2051864856","https://openalex.org/W2054726326","https://openalex.org/W2057013716","https://openalex.org/W2057843068","https://openalex.org/W2059093611","https://openalex.org/W2067236515","https://openalex.org/W2073564607","https://openalex.org/W2081724315","https://openalex.org/W2082148481","https://openalex.org/W2087495141","https://openalex.org/W2092247420","https://openalex.org/W2093795463","https://openalex.org/W2105385262","https://openalex.org/W2109540804","https://openalex.org/W2115443902","https://openalex.org/W2119267663","https://openalex.org/W2122943946","https://openalex.org/W2123746949","https://openalex.org/W2126157913","https://openalex.org/W2128577591","https://openalex.org/W2130863822","https://openalex.org/W2130897905","https://openalex.org/W2132820240","https://openalex.org/W2138613375","https://openalex.org/W2139230158","https://openalex.org/W2139236870","https://openalex.org/W2139281871","https://openalex.org/W2139915497","https://openalex.org/W2142695681","https://openalex.org/W2153654642","https://openalex.org/W2155147384","https://openalex.org/W2155839962","https://openalex.org/W2157654386","https://openalex.org/W2159446746","https://openalex.org/W2160535028","https://openalex.org/W2162276362","https://openalex.org/W2173769259","https://openalex.org/W2324081924","https://openalex.org/W2413334978","https://openalex.org/W2419396195","https://openalex.org/W2487854154","https://openalex.org/W3103106703"],"related_works":["https://openalex.org/W2260493136","https://openalex.org/W2113188411","https://openalex.org/W4210423528","https://openalex.org/W2095205630","https://openalex.org/W2976965029","https://openalex.org/W2939859775","https://openalex.org/W2160020195","https://openalex.org/W2055827177","https://openalex.org/W2023600921","https://openalex.org/W2382178265"],"abstract_inverted_index":{"The":[0,69,137],"CABS":[1,25],"coarse-grained":[2],"model":[3,52,139],"is":[4,140],"a":[5,141],"well-established":[6],"tool":[7],"for":[8,83,144],"modeling":[9,33,148],"globular":[10],"proteins":[11,61,89],"(predicting":[12],"their":[13,67,91],"structure,":[14],"dynamics,":[15],"and":[16,27,81,134],"interactions).":[17],"Here":[18],"we":[19,101],"introduce":[20],"an":[21],"extension":[22],"of":[23,34,37,45,56,86,149],"the":[24,32,35,38,43,50,78,87,95,98,107,116,131],"representation":[26,133],"force":[28],"field":[29],"(CABS-membrane)":[30],"to":[31,106,114,130],"effect":[36],"biological":[39],"membrane":[40,46,60,79,109],"environment":[41,80],"on":[42],"structure":[44],"proteins.":[47],"We":[48,111],"validate":[49],"CABS-membrane":[51,138],"in":[53],"folding":[54],"simulations":[55,70],"10":[57],"short":[58],"helical":[59],"not":[62],"using":[63,120],"any":[64],"knowledge":[65],"about":[66],"structure.":[68],"start":[71],"from":[72],"random":[73],"protein":[74],"conformations":[75],"placed":[76],"outside":[77],"allow":[82],"full":[84],"flexibility":[85],"modeled":[88],"during":[90],"spontaneous":[92],"insertion":[93],"into":[94],"membrane.":[96],"In":[97],"resulting":[99],"trajectories,":[100],"have":[102],"found":[103],"models":[104,119],"close":[105],"experimental":[108],"structures.":[110],"also":[112],"attempted":[113],"select":[115],"correctly":[117],"folded":[118],"simple":[121],"filtering":[122],"followed":[123],"by":[124],"structural":[125],"clustering":[126],"combined":[127],"with":[128],"reconstruction":[129],"all-atom":[132,135],"scoring.":[136],"promising":[142],"approach":[143],"further":[145],"development":[146],"toward":[147],"large":[150],"protein\u2013membrane":[151],"systems.":[152]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":10}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-10-28T00:00:00"}