{"doi":"10.1098/rsfs.2018.0081","title":"MS2 bacteriophage capsid studied using all-atom molecular dynamics","abstract":"<jats:p>The all-atom model of an MS2 bacteriophage particle without its genome (the capsid) was built using high-resolution cryo-electron microscopy (EM) measurements for initial conformation. The structural characteristics of the capsid and the dynamics of the surrounding solution were examined using molecular dynamics simulation. The model demonstrates the overall preservation of the cryo-EM structure of the capsid at physiological conditions (room temperature and ions composition). The formation of a dense anion layer near the inner surface and a diffuse cation layer near the outer surface of the capsid was detected. The flow of water molecules and ions across the capsid through its pores were quantified, which was considerable for water and substantial for ions.</jats:p>","journal":"Interface Focus","year":2019,"id":15570,"datarank":1.028623367047619,"base_score":3.4339872044851463,"endowment":3.4339872044851463,"self_citation_contribution":0.515098080672772,"citation_network_contribution":0.5135252863748472,"self_endowment_contribution":0.515098080672772,"citer_contribution":0.5135252863748472,"corpus_percentile":null,"corpus_rank":null,"citation_count":30,"citer_count":23,"citers_with_citation_signal":19,"citers_with_endowment":19,"datacite_reuse_total":6,"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":118380,"name":"Dmitry Nerukh","orcid":"0000-0001-9005-9919","position":1,"is_corresponding":false},{"id":118379,"name":"Vladimir S. Farafonov","orcid":"0000-0003-0785-9582","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":3.4339872044851463,"endowment":3.4339872044851463,"datacite_reuse_total":6,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"31065345","pmcid":"PMC6501343","openalex_id":"https://openalex.org/W2938650863","authors":[],"funders":[{"funder_name":"Ministry of Education and Science of Ukraine","grant_id":"0117U004966","title":null},{"funder_name":"Engineering and Physical Sciences Research Council","grant_id":"EP/P020232/1","title":"Proposal for a Tier 2 Centre - HPC Midlands Plus"},{"funder_name":"Japan Society for the Promotion of Science","grant_id":"BR170303","title":null}],"total_grants":3,"fwci":3.1219,"citation_percentile":0.91243576,"influential_citations":0,"citation_trend":[{"year":2019,"count":2},{"year":2020,"count":3},{"year":2021,"count":5},{"year":2022,"count":8},{"year":2023,"count":5},{"year":2024,"count":3},{"year":2025,"count":3},{"year":2026,"count":1}],"oa_status":"bronze","license":"Royal Society Data Sharing and Accessibility","oa_locations":[{"url":"https://royalsocietypublishing.org/doi/pdf/10.1098/rsfs.2018.0081","host_type":"journal"},{"url":"https://royalsocietypublishing.org/doi/pdf/10.1098/rsfs.2018.0081","host_type":"BRONZE"},{"url":"https://royalsocietypublishing.org/doi/pdf/10.1098/rsfs.2018.0081","host_type":"publisher"},{"url":"https://royalsocietypublishing.org/doi/full-xml/10.1098/rsfs.2018.0081","host_type":"publisher"},{"url":"https://doi.org/10.1098/rsfs.2018.0081","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/31065345","host_type":"repository"},{"url":"https://publications.aston.ac.uk/view/author/82493c64386d13c53decf52ccb2dad5f.html>","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6501343","host_type":"repository"},{"url":"https://publications.aston.ac.uk/id/eprint/39020/1/manuscript_revised.pdf","host_type":"repository"},{"url":"https://dx.doi.org/10.1098/rsfs.2018.0081","host_type":""}],"fields_of_study":["Bacteriophages and microbial interactions","Spectroscopy and Quantum Chemical Studies","Nanopore and Nanochannel Transport Studies","Medicine","Chemistry","Physics","Biology","Materials Science","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":[],"keywords":["Capsid","Bacteriophage","Molecular dynamics","Ion","Bacteriophage MS2","Cryo-electron microscopy","Chemical physics","Resolution (logic)","Particle (ecology)","Molecule","Atom (system on chip)","Materials science","Chemistry","Biophysics","Crystallography","Biology","Escherichia coli","Computational chemistry","Gene","Biochemistry","Computer science","Ms2 Virus Capsid","Flow Of Solution","Ions Distribution"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Clean water and sanitation"}],"linked_datasets":[{"doi":"10.6084/m9.figshare.7879262.v1","title":"Details on the simulation model preparation from MS2 bacteriophage capsid studied using all-atom molecular dynamics","publisher":"The Royal Society","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.7879262.v2","title":"Details on the simulation model preparation from MS2 bacteriophage capsid studied using all-atom molecular dynamics.","publisher":"The Royal Society","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.7879262","title":"Details on the simulation model preparation from MS2 bacteriophage capsid studied using all-atom molecular dynamics.","publisher":"The Royal Society","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.c.4444457.v2","title":"Supplementary material from \"MS2 bacteriophage capsid studied using all-atom molecular dynamics\"","publisher":"Figshare","resource_type":"Collection"},{"doi":"10.6084/m9.figshare.c.4444457.v1","title":"Supplementary material from \"MS2 bacteriophage capsid studied using all-atom molecular dynamics\"","publisher":"Figshare","resource_type":"Collection"},{"doi":"10.6084/m9.figshare.c.4444457","title":"Supplementary material from \"MS2 bacteriophage capsid studied using all-atom molecular dynamics\"","publisher":"Figshare","resource_type":"Collection"}],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"pdb"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-01T18:13:29.946214Z","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":[]}