2026-10-07T10:02:12Z https://api.figshare.com/v2/oai

oai:figshare.com:article/34037094 2026-09-30T22:40:06Z category_24703 category_25258 category_25198 item_type_2 month_year_09_2026

Molecular Dynamics Trajectory Movies and Cluster-Resolved Data for Five Flaviviral NS5–Ligand Complexes Ayesh Madushanka Mahamada Kalapuwage (18778009) Dhanudhdhara Gamage (24607058) Elfi Kraka (8883960) Medical virology Computational chemistry Medicinal and biomolecular chemistry not elsewhere classified molecular dynamics Flavivirus Antiviral DENV ZIKV WNV YFV JEV QM/MM <p dir="ltr">This dataset contains molecular dynamics (MD) trajectory movies and associated cluster-resolved data for five flaviviral NS5–ligand complexes investigated using molecular dynamics, binding-site-guided conformational clustering, quantum mechanics/molecular mechanics (QM/MM) calculations, and local vibrational mode analysis (LMA).</p><p dir="ltr">The five systems are: (1) dengue virus (DENV)–Fungisterol, (2) Zika virus (ZIKV)–Curcumin, (3) West Nile virus (WNV)–Cholic acid, (4) yellow fever virus (YFV)–Fungisterol, and (5) Japanese encephalitis virus (JEV)–Cholic acid.</p><p dir="ltr">Each selected complex was subjected to molecular dynamics simulation, and binding-site-guided clustering was subsequently used to identify five representative ligand–binding-pocket conformations (C1–C5). These representative structures were used for subsequent QM/MM and local vibrational mode analyses to characterize conformational variation in the noncovalent ligand–protein interaction networks.</p><p dir="ltr">The deposited MD movies provide visualization of the conformational dynamics sampled by the five selected systems. Associated machine-readable data provide information supporting the conformational clustering and interaction analyses reported in the accompanying manuscript.</p><p dir="ltr">The large trajectory visualization files are deposited through Figshare rather than included directly in the Supporting Information of the manuscript.</p> 2026-09-30T22:40:06Z Dataset Media 10.6084/m9.figshare.34037094.v1 https://figshare.com/articles/media/Molecular_Dynamics_Trajectory_Movies_and_Cluster-Resolved_Data_for_Five_Flaviviral_NS5_Ligand_Complexes/34037094 CC BY 4.0