{"doi":"10.1002/jcc.25773","title":"CHARMM‐GUI <i>Nanodisc Builder</i> for modeling and simulation of various nanodisc systems","abstract":"<jats:p>Nanodiscs are discoidal protein–lipid complexes that have wide applications in membrane protein studies. Modeling and simulation of nanodiscs are challenging due to the absence of structures of many membrane scaffold proteins (MSPs) that wrap around the membrane bilayer. We have developed CHARMM‐GUI <jats:italic>Nanodisc Builder</jats:italic> (<jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"http://www.charmm-gui.org/input/nanodisc\">http://www.charmm-gui.org/input/nanodisc</jats:ext-link>) to facilitate the setup of nanodisc simulation systems by modeling the MSPs with defined size and known structural features. A total of 11 different nanodiscs with a diameter from 80 to 180 Å are made available in both the all‐atom CHARMM and two coarse‐grained (PACE and Martini) force fields. The usage of the <jats:italic>Nanodisc Builder</jats:italic> is demonstrated with various simulation systems. The structures and dynamics of proteins and lipids in these systems were analyzed, showing similar behaviors to those from previous all‐atom and coarse‐grained nanodisc simulations. We expect the <jats:italic>Nanodisc Builder</jats:italic> to be a convenient and reliable tool for modeling and simulation of nanodisc systems. © 2019 Wiley Periodicals, Inc.</jats:p>","journal":"Journal of Computational Chemistry","year":2019,"id":650023,"datarank":0.6456097639806255,"base_score":4.304065093204169,"endowment":4.304065093204169,"self_citation_contribution":0.6456097639806255,"citation_network_contribution":0.0,"self_endowment_contribution":0.6456097639806255,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":73,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":383003,"name":"Jumin Lee","orcid":"0000-0002-1008-0118","position":1,"is_corresponding":false},{"id":308076,"name":"Jeffery B. Klauda","orcid":"0000-0001-8725-1870","position":2,"is_corresponding":false},{"id":56772,"name":"Wonpil Im","orcid":"0000-0001-5642-6041","position":3,"is_corresponding":false},{"id":115277,"name":"Yifei Qi","orcid":"0000-0003-2853-7910","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"CHARMM‐GUI <i>Nanodisc Builder</i> for modeling and simulation of various nanodisc systems","abstract":"<jats:p>Nanodiscs are discoidal protein–lipid complexes that have wide applications in membrane protein studies. Modeling and simulation of nanodiscs are challenging due to the absence of structures of many membrane scaffold proteins (MSPs) that wrap around the membrane bilayer. We have developed CHARMM‐GUI <jats:italic>Nanodisc Builder</jats:italic> (<jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"http://www.charmm-gui.org/input/nanodisc\">http://www.charmm-gui.org/input/nanodisc</jats:ext-link>) to facilitate the setup of nanodisc simulation systems by modeling the MSPs with defined size and known structural features. A total of 11 different nanodiscs with a diameter from 80 to 180 Å are made available in both the all‐atom CHARMM and two coarse‐grained (PACE and Martini) force fields. The usage of the <jats:italic>Nanodisc Builder</jats:italic> is demonstrated with various simulation systems. The structures and dynamics of proteins and lipids in these systems were analyzed, showing similar behaviors to those from previous all‐atom and coarse‐grained nanodisc simulations. We expect the <jats:italic>Nanodisc Builder</jats:italic> to be a convenient and reliable tool for modeling and simulation of nanodisc systems. © 2019 Wiley Periodicals, Inc.</jats:p>","is_dataset_classified":null,"base_score":4.304065093204169,"endowment":4.304065093204169,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"30677169","pmcid":null,"openalex_id":"https://openalex.org/W2913254604","authors":[],"funders":[{"funder_name":"Division of Biological Infrastructure","grant_id":"1660380","title":null},{"funder_name":"Division of Biological Infrastructure","grant_id":"1707207","title":null},{"funder_name":"Division of Molecular and Cellular Biosciences","grant_id":"1149187","title":null},{"funder_name":"Division of Molecular and Cellular Biosciences","grant_id":"1727508","title":null},{"funder_name":"Division of Molecular and Cellular Biosciences","grant_id":"1810695","title":null},{"funder_name":"National Institute of General Medical Sciences","grant_id":"GM087519","title":null},{"funder_name":"National Institute of General Medical Sciences","grant_id":"GM103695","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"31700646","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"MCB‐1149187","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"XSEDE MCB070009","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"R01 GM103695","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"U54 GM087519","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"DBI‐1660380","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"DBI‐1707207","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"MCB‐1727508","title":null},{"funder_name":"National Natural Science Foundation of China","grant_id":"MCB‐1810695","title":null}],"total_grants":16,"fwci":2.4336,"citation_percentile":0.89957958,"influential_citations":0,"citation_trend":[{"year":2019,"count":7},{"year":2020,"count":7},{"year":2021,"count":9},{"year":2022,"count":9},{"year":2023,"count":12},{"year":2024,"count":7},{"year":2025,"count":12},{"year":2026,"count":10}],"oa_status":"closed","license":"http://onlinelibrary.wiley.com/termsAndConditions#am","oa_locations":[{"url":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fjcc.25773","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.25773","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.25773","host_type":"publisher"},{"url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jcc.25773","host_type":"publisher"},{"url":"https://doi.org/10.1002/jcc.25773","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/30677169","host_type":"repository"}],"fields_of_study":["Advanced biosensing and bioanalysis techniques","Lipid Membrane Structure and Behavior","Nanopore and Nanochannel Transport Studies","Computer Simulation","Lipids","Models, Chemical","Nanoparticles","Proteins"],"mesh_terms":["Computer Simulation","Lipids","Models, Chemical","Proteins","Nanoparticles"],"keywords":["Nanodisc","Molecular dynamics","Chemistry","Biophysics","Lipid bilayer","Computer science","Membrane","Biochemistry","Biology","Computational chemistry","Membrane protein","Membrane Scaffold Protein","Lipid Diffusion"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-10T04:43:30.116143Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}