{"doi":"10.1101/2020.05.20.103325","title":"Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane","abstract":"This technical study describes all-atom modeling and simulation of a fully-glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB:6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXY modeling suite. Then, using the recently-determined most occupied glycoforms, 22 N-glycans and 1 O-glycan of each monomer were modeled using Glycan Reader & Modeler in CHARMM-GUI. These fully-glycosylated full-length S protein model structures were assessed and further refined against the low-resolution data in their respective experimental maps using ISOLDE. We then used CHARMM-GUI Membrane Builder to place the S proteins in a viral membrane and performed all-atom molecular dynamics simulations. All structures are available in CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19), so researchers can use these models to carry out innovative and novel modeling and simulation research for the prevention and treatment of COVID-19.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":122767,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8417,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":565382,"name":"Sang-Jun Park","orcid":null,"position":1,"is_corresponding":false},{"id":383002,"name":"Yeol Kyo Choi","orcid":"0000-0002-4218-7139","position":2,"is_corresponding":false},{"id":565383,"name":"Taeyong Park","orcid":null,"position":3,"is_corresponding":false},{"id":565384,"name":"Maham Tanveer","orcid":null,"position":4,"is_corresponding":false},{"id":565385,"name":"Yiwei Cao","orcid":null,"position":5,"is_corresponding":false},{"id":565386,"name":"Nathan R. Kern","orcid":null,"position":6,"is_corresponding":false},{"id":383003,"name":"Jumin Lee","orcid":"0000-0002-1008-0118","position":7,"is_corresponding":false},{"id":564602,"name":"Min Sun Yeom","orcid":"0000-0001-9977-8768","position":8,"is_corresponding":false},{"id":103425,"name":"Tristan I. Croll","orcid":"0000-0002-3514-8377","position":9,"is_corresponding":false},{"id":217344,"name":"Chaok Seok","orcid":"0000-0002-1419-9888","position":10,"is_corresponding":false},{"id":56772,"name":"Wonpil Im","orcid":"0000-0001-5642-6041","position":11,"is_corresponding":false},{"id":199021,"name":"Hyeonuk Woo","orcid":"0000-0002-6495-4087","position":0,"is_corresponding":true}],"reference_count":59,"raw_metadata":null,"created_at":"2026-07-18T23:14:55.385653Z","pmid":"32511389","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":[]}