{"id":"https://openalex.org/W2945514040","doi":"https://doi.org/10.1093/nar/gkz416","title":"MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics","display_name":"MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics","publication_year":2019,"publication_date":"2019-05-06","ids":{"openalex":"https://openalex.org/W2945514040","doi":"https://doi.org/10.1093/nar/gkz416","mag":"2945514040","pmid":"https://pubmed.ncbi.nlm.nih.gov/31106328"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkz416","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz416","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W456/28879794/gkz416.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/47/W1/W456/28879794/gkz416.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073258672","display_name":"Mangesh Damre","orcid":"https://orcid.org/0000-0002-4371-3815"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]},{"id":"https://openalex.org/I138549579","display_name":"Scuola Internazionale Superiore di Studi Avanzati","ror":"https://ror.org/004fze387","country_code":"IT","type":"education","lineage":["https://openalex.org/I138549579"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mangesh Damre","raw_affiliation_strings":["Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy","Neurobiology, International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy"],"raw_orcid":"https://orcid.org/0000-0002-4371-3815","affiliations":[{"raw_affiliation_string":"Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy","institution_ids":["https://openalex.org/I119439378"]},{"raw_affiliation_string":"Neurobiology, International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy","institution_ids":["https://openalex.org/I138549579"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003793114","display_name":"Alessandro Marchetto","orcid":"https://orcid.org/0000-0001-9857-4376"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessandro Marchetto","raw_affiliation_strings":["Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy","institution_ids":["https://openalex.org/I119439378"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101510898","display_name":"Alejandro Giorgetti","orcid":"https://orcid.org/0000-0001-8738-6150"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]},{"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"]}],"countries":["DE","IT"],"is_corresponding":true,"raw_author_name":"Alejandro Giorgetti","raw_affiliation_strings":["Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy","Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum J\u00fclich, 52428 J\u00fclich, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie, 15, 37134 Verona, Italy","institution_ids":["https://openalex.org/I119439378"]},{"raw_affiliation_string":"Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum J\u00fclich, 52428 J\u00fclich, Germany","institution_ids":["https://openalex.org/I171892758"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101510898"],"corresponding_institution_ids":["https://openalex.org/I119439378","https://openalex.org/I171892758"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.9792,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.85073038,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"47","issue":"W1","first_page":"W456","last_page":"W461"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical 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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9983999729156494,"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/biology","display_name":"Biology","score":0.9246956706047058},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5767906308174133},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5509419441223145},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39754047989845276},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.38297200202941895},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.333913117647171},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.16247698664665222},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.05861690640449524}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9246956706047058},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5767906308174133},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5509419441223145},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39754047989845276},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.38297200202941895},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.333913117647171},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.16247698664665222},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.05861690640449524},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":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}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkz416","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz416","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W456/28879794/gkz416.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:31106328","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31106328","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:5577323","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6602572","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkz416","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz416","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W456/28879794/gkz416.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320324120","display_name":"Universit\u00e0 degli Studi di Verona","ror":"https://ror.org/039bp8j42"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2945514040.pdf","grobid_xml":"https://content.openalex.org/works/W2945514040.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1984876295","https://openalex.org/W2002479689","https://openalex.org/W2008708467","https://openalex.org/W2021520922","https://openalex.org/W2038995335","https://openalex.org/W2054546169","https://openalex.org/W2069152576","https://openalex.org/W2097775366","https://openalex.org/W2119267663","https://openalex.org/W2127821584","https://openalex.org/W2130479394","https://openalex.org/W2155841258","https://openalex.org/W2168909179","https://openalex.org/W2171012684","https://openalex.org/W2171268876","https://openalex.org/W2295059836","https://openalex.org/W2314292783","https://openalex.org/W2319900881","https://openalex.org/W2327174080","https://openalex.org/W2414242907","https://openalex.org/W2468453423","https://openalex.org/W2766539659","https://openalex.org/W2767727552","https://openalex.org/W2788954552","https://openalex.org/W2802007263","https://openalex.org/W2910356247","https://openalex.org/W3099088600"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2065457896","https://openalex.org/W3173234801","https://openalex.org/W2167984027","https://openalex.org/W3021302227","https://openalex.org/W10630519","https://openalex.org/W1919377569","https://openalex.org/W3144288563","https://openalex.org/W3123907821","https://openalex.org/W2382319620"],"abstract_inverted_index":{"Atomistic":[0],"molecular":[1,17,64,97],"dynamics":[2,81,98],"simulations":[3,100],"of":[4,30,61],"membrane":[5,34,79],"proteins":[6],"have":[7],"been":[8,48],"shown":[9,49],"to":[10,92,102],"be":[11],"extremely":[12],"useful":[13],"for":[14],"characterizing":[15],"the":[16,28,76,90,104],"features":[18],"underlying":[19,66],"their":[20],"function,":[21],"but":[22],"require":[23],"high":[24],"computational":[25,56],"power,":[26,57],"limiting":[27],"understanding":[29],"complex":[31],"events":[32,65],"in":[33,70],"proteins,":[35],"e.g.":[36],"ion":[37],"channels":[38],"gating,":[39],"GPCRs":[40],"activation.":[41],"To":[42],"overcome":[43],"this":[44],"issue,":[45],"it":[46],"has":[47],"that":[50,88],"coarse-grained":[51,78,96],"approaches,":[52],"although":[53],"requiring":[54],"less":[55],"are":[58],"still":[59],"capable":[60],"correctly":[62],"describing":[63],"big":[67],"conformational":[68],"changes":[69],"biological":[71],"systems.":[72],"Here,":[73],"we":[74],"present":[75],"Martini":[77],"protein":[80],"(MERMAID),":[82],"a":[83],"publicly":[84],"available":[85],"web":[86],"interface":[87],"allows":[89],"user":[91],"prepare":[93],"and":[94,101],"run":[95],"(CGMD)":[99],"analyse":[103],"trajectories.":[105]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}