{"id":"https://openalex.org/W4320855360","doi":"https://doi.org/10.1093/bib/bbad057","title":"MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations","display_name":"MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations","publication_year":2023,"publication_date":"2023-02-15","ids":{"openalex":"https://openalex.org/W4320855360","doi":"https://doi.org/10.1093/bib/bbad057","pmid":"https://pubmed.ncbi.nlm.nih.gov/36790845"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad057","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad057","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5061120915","display_name":"Hui Liu","orcid":"https://orcid.org/0000-0002-1267-2475"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I4210157677","display_name":"Hubei Academy of Agricultural Sciences","ror":"https://ror.org/04qg81z57","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210157677"]},{"id":"https://openalex.org/I75900474","display_name":"Hubei University","ror":"https://ror.org/03a60m280","country_code":"CN","type":"education","lineage":["https://openalex.org/I75900474"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hui Liu","raw_affiliation_strings":["Huazhong Agricultural University , College of Informatics, , Wuhan, Hubei 430070 , China","Hubei Key Laboratory of Agricultural Bioinformatics , College of Informatics, , Wuhan, Hubei 430070 , China","Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China"],"affiliations":[{"raw_affiliation_string":"Huazhong Agricultural University , College of Informatics, , Wuhan, Hubei 430070 , China","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics , College of Informatics, , Wuhan, Hubei 430070 , China","institution_ids":["https://openalex.org/I4210157677","https://openalex.org/I75900474"]},{"raw_affiliation_string":"Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102918060","display_name":"Ye Jin","orcid":"https://orcid.org/0009-0006-6445-9955"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ye Jin","raw_affiliation_strings":["Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University , Suzhou, Jiangsu 215123 , China"],"affiliations":[{"raw_affiliation_string":"Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University , Suzhou, Jiangsu 215123 , China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111910143","display_name":"Hanjing Ding","orcid":null},"institutions":[{"id":"https://openalex.org/I4210101555","display_name":"Hubei University of Science and Technology","ror":"https://ror.org/018wg9441","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210101555"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hanjing Ding","raw_affiliation_strings":["School of Basic Medical Sciences, Hubei University of Science and Technology , Xianning, Hubei 437100 , China"],"affiliations":[{"raw_affiliation_string":"School of Basic Medical Sciences, Hubei University of Science and Technology , Xianning, Hubei 437100 , China","institution_ids":["https://openalex.org/I4210101555"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5061120915","https://openalex.org/A5111910143"],"corresponding_institution_ids":["https://openalex.org/I204823248","https://openalex.org/I4210101555","https://openalex.org/I4210157677","https://openalex.org/I75900474"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.5794,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.89505518,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"24","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9975000023841858,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.9045613408088684},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8302595615386963},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8234062194824219},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5900081992149353},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5501617789268494},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.47903385758399963},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.46430614590644836},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4227296710014343},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.3927944004535675},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.39201197028160095},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.38291478157043457},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3534785509109497},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.336811900138855}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.9045613408088684},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8302595615386963},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8234062194824219},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5900081992149353},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5501617789268494},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.47903385758399963},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.46430614590644836},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4227296710014343},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.3927944004535675},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.39201197028160095},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.38291478157043457},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3534785509109497},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.336811900138855}],"mesh":[{"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":"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":2,"locations":[{"id":"doi:10.1093/bib/bbad057","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad057","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36790845","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36790845","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.41999998688697815,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G7291291478","display_name":null,"funder_award_id":"2662022XXYJ010","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1526205344","https://openalex.org/W1969231606","https://openalex.org/W1976203248","https://openalex.org/W2010822348","https://openalex.org/W2021520922","https://openalex.org/W2029667189","https://openalex.org/W2050333027","https://openalex.org/W2082586732","https://openalex.org/W2093221728","https://openalex.org/W2098055048","https://openalex.org/W2103325328","https://openalex.org/W2109872885","https://openalex.org/W2118233996","https://openalex.org/W2119941807","https://openalex.org/W2121400889","https://openalex.org/W2132262459","https://openalex.org/W2146292423","https://openalex.org/W2150981663","https://openalex.org/W2160544821","https://openalex.org/W2568617656","https://openalex.org/W6631666057"],"related_works":["https://openalex.org/W207660752","https://openalex.org/W3121352828","https://openalex.org/W2132241624","https://openalex.org/W4386463918","https://openalex.org/W3042795425","https://openalex.org/W4311683883","https://openalex.org/W4226330600","https://openalex.org/W4221030787","https://openalex.org/W4212902261","https://openalex.org/W2790811106"],"abstract_inverted_index":{"The":[0,114,137],"preprocessed":[1],"initial":[2],"files":[3,103],"that":[4,54],"feed":[5],"the":[6,14,17,20,31,35,59,79,101,124,151],"molecular":[7],"dynamics":[8],"(MD)":[9],"simulation":[10,23,39,66,112],"packages":[11,24],"dramatically":[12],"influence":[13],"outcome":[15],"of":[16,37,142],"simulations.":[18],"However,":[19],"popular":[21,64],"MD":[22,38,65,75,111],"depend,":[25],"to":[26,73,77,94,99],"a":[27,51,85,120],"great":[28],"extent,":[29],"on":[30,132],"user's":[32],"experience":[33],"in":[34,57],"preparation":[36],"systems.":[40],"In":[41],"this":[42],"work,":[43],"we":[44],"present":[45],"an":[46,96],"easy-to-use":[47],"tool":[48],"called":[49],"MDBuilder,":[50],"PyMOL":[52,121],"plugin":[53,122],"assists":[55],"researchers":[56],"building":[58],"starting":[60],"structures":[61],"for":[62,104],"multiple":[63],"packages.":[67,113],"MDBuilder":[68,143],"is":[69,117],"not":[70],"only":[71],"designed":[72],"assist":[74],"beginners":[76],"overcome":[78],"steep":[80],"learning":[81],"curve":[82],"by":[83],"providing":[84],"menu-oriented,":[86],"point-and-click":[87],"user":[88],"graphic":[89],"interface":[90],"(GUI),":[91],"but":[92],"also":[93],"provide":[95],"alternative":[97],"way":[98],"prepare":[100],"input":[102],"some":[105],"highly":[106],"scalable":[107],"CHARMM":[108],"force":[109],"field-based":[110],"platform-independent":[115],"GUI":[116],"implemented":[118],"as":[119],"using":[123],"Python":[125],"language,":[126],"and":[127,134,140],"it":[128],"has":[129],"been":[130],"tested":[131],"Windows":[133],"Linux":[135],"platforms.":[136],"source":[138],"code":[139],"documentation":[141],"can":[144],"be":[145],"downloaded":[146],"freely":[147],"from":[148],"https://github.com/HuiLiuCode/MDBuilder":[149],"under":[150],"GNU":[152],"General":[153],"Public":[154],"License.":[155]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6}],"updated_date":"2026-03-01T08:55:55.761014","created_date":"2025-10-10T00:00:00"}