{"id":"https://openalex.org/W2952857611","doi":"https://doi.org/10.1186/s12859-017-1541-z","title":"Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP","display_name":"Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP","publication_year":2017,"publication_date":"2017-02-20","ids":{"openalex":"https://openalex.org/W2952857611","doi":"https://doi.org/10.1186/s12859-017-1541-z","mag":"2952857611","pmid":"https://pubmed.ncbi.nlm.nih.gov/28219343"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1541-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1541-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1541-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1541-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006314973","display_name":"Julia Koehler Leman","orcid":"https://orcid.org/0000-0002-5693-3593"},"institutions":[{"id":"https://openalex.org/I4210153546","display_name":"Flatiron Health (United States)","ror":"https://ror.org/0508h6p74","country_code":"US","type":"company","lineage":["https://openalex.org/I4210153546"]},{"id":"https://openalex.org/I4387153999","display_name":"Flatiron Institute","ror":"https://ror.org/00sekdz59","country_code":null,"type":"nonprofit","lineage":["https://openalex.org/I4210107338","https://openalex.org/I4387153999"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Julia Koehler Leman","raw_affiliation_strings":["Center for Computational Biology, Flatiron Institute, 162 Fifth Avenue, New York, NY, 10010, USA. julia.koehler.leman@gmail.com","Departments of Biology and Computer Science, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. julia.koehler.leman@gmail.com","Center for Computational Biology, Flatiron Institute, 162 Fifth Avenue, New York, NY, 10010, USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Flatiron Institute, 162 Fifth Avenue, New York, NY, 10010, USA. julia.koehler.leman@gmail.com","institution_ids":[]},{"raw_affiliation_string":"Departments of Biology and Computer Science, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA. julia.koehler.leman@gmail.com","institution_ids":[]},{"raw_affiliation_string":"Center for Computational Biology, Flatiron Institute, 162 Fifth Avenue, New York, NY, 10010, USA","institution_ids":["https://openalex.org/I4210153546","https://openalex.org/I4387153999"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075127527","display_name":"Sergey Lyskov","orcid":"https://orcid.org/0000-0001-6380-6712"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergey Lyskov","raw_affiliation_strings":["Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055203249","display_name":"Richard Bonneau","orcid":"https://orcid.org/0000-0003-4354-7906"},"institutions":[{"id":"https://openalex.org/I4210153546","display_name":"Flatiron Health (United States)","ror":"https://ror.org/0508h6p74","country_code":"US","type":"company","lineage":["https://openalex.org/I4210153546"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]},{"id":"https://openalex.org/I4387153999","display_name":"Flatiron Institute","ror":"https://ror.org/00sekdz59","country_code":null,"type":"nonprofit","lineage":["https://openalex.org/I4210107338","https://openalex.org/I4387153999"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard Bonneau","raw_affiliation_strings":["Center for Computational Biology, Flatiron Institute, 162 Fifth Avenue, New York, NY, 10010, USA","Departments of Biology and Computer Science, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA"],"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, Flatiron Institute, 162 Fifth Avenue, New York, NY, 10010, USA","institution_ids":["https://openalex.org/I4210153546","https://openalex.org/I4387153999"]},{"raw_affiliation_string":"Departments of Biology and Computer Science, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA","institution_ids":["https://openalex.org/I57206974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5006314973"],"corresponding_institution_ids":["https://openalex.org/I4210153546","https://openalex.org/I4387153999"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.2982,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.80460383,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"18","issue":"1","first_page":"115","last_page":"115"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9976000189781189,"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":0.9976000189781189,"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":0.9972000122070312,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.989300012588501,"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-protein","display_name":"Membrane protein","score":0.5470978021621704},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46406421065330505},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4547927975654602},{"id":"https://openalex.org/keywords/lipid-bilayer","display_name":"Lipid bilayer","score":0.42833077907562256},{"id":"https://openalex.org/keywords/lipid-metabolism","display_name":"Lipid metabolism","score":0.41531819105148315},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.3591393828392029},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3220248520374298},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2959807515144348},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.29303908348083496},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2464596927165985}],"concepts":[{"id":"https://openalex.org/C144647389","wikidata":"https://www.wikidata.org/wiki/Q423042","display_name":"Membrane protein","level":3,"score":0.5470978021621704},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46406421065330505},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4547927975654602},{"id":"https://openalex.org/C39944091","wikidata":"https://www.wikidata.org/wiki/Q423279","display_name":"Lipid bilayer","level":3,"score":0.42833077907562256},{"id":"https://openalex.org/C4733338","wikidata":"https://www.wikidata.org/wiki/Q2792936","display_name":"Lipid metabolism","level":2,"score":0.41531819105148315},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3591393828392029},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3220248520374298},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2959807515144348},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.29303908348083496},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2464596927165985}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008055","descriptor_name":"Lipids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008055","descriptor_name":"Lipids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008055","descriptor_name":"Lipids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008055","descriptor_name":"Lipids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D012997","descriptor_name":"Solvents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-017-1541-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1541-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1541-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28219343","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28219343","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:4177867","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5319049","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5319049","is_oa":true,"landing_page_url":"http://doi.org/10.1186/s12859-017-1541-z","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1541-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1541-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1541-z","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.44999998807907104,"id":"https://metadata.un.org/sdg/6","display_name":"Clean water and sanitation"}],"awards":[{"id":"https://openalex.org/G7098145897","display_name":null,"funder_award_id":"NIH R01-GM073151","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306164","display_name":"Simons Foundation","ror":"https://ror.org/01cmst727"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2952857611.pdf","grobid_xml":"https://content.openalex.org/works/W2952857611.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1544009106","https://openalex.org/W1605284188","https://openalex.org/W1879820513","https://openalex.org/W1915750328","https://openalex.org/W1987592565","https://openalex.org/W1989109406","https://openalex.org/W1992657771","https://openalex.org/W2008708467","https://openalex.org/W2022523297","https://openalex.org/W2051872583","https://openalex.org/W2053448121","https://openalex.org/W2099057076","https://openalex.org/W2105537627","https://openalex.org/W2116807248","https://openalex.org/W2122510434","https://openalex.org/W2125872855","https://openalex.org/W2127268158","https://openalex.org/W2129838159","https://openalex.org/W2131284518","https://openalex.org/W2140831051","https://openalex.org/W2143059772","https://openalex.org/W2151156268","https://openalex.org/W2153504150","https://openalex.org/W2154882487","https://openalex.org/W2155839962","https://openalex.org/W2157380138","https://openalex.org/W2158412800","https://openalex.org/W2159522826","https://openalex.org/W2160838977","https://openalex.org/W2162274915","https://openalex.org/W2169242540","https://openalex.org/W4251391716","https://openalex.org/W4293003482"],"related_works":["https://openalex.org/W4378232245","https://openalex.org/W2745652071","https://openalex.org/W4389719889","https://openalex.org/W4388673097","https://openalex.org/W2622562234","https://openalex.org/W2802815821","https://openalex.org/W3127134208","https://openalex.org/W2011028086","https://openalex.org/W2422656563","https://openalex.org/W1493374012"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2}],"updated_date":"2026-03-09T08:58:05.943551","created_date":"2019-06-27T00:00:00"}
