ev a71 strain h vr 1432  (ATCC)

Journal: Cell Reports Physical Science

Article Title: Antiviral discovery using sparse datasets by integrating experiments, molecular simulations, and machine learning

doi: 10.1016/j.xcrp.2025.102554

Figure Lengend Snippet: Figure 1. Experimental workflow and virucidal activity of chemical compounds against EV71 (A) Schematic representation of the experimental procedures adopted to build the low-density in-house dataset for the ML model. (B) In-house dataset: virucidal activity, expressed as log10(PFU mL1) reduction, of each chemical toward the EV71 ATCC VR-1432 strain. Black cells within the heatmap represent conditions not tested because the compound was insoluble at that pH. Data represent the mean of two independent experiments, each conducted in duplicate. The tree structure was generated based on the Euclidean distance matrix of compound latent codes of the variational autoencoder (VAE) that led to the best regression model (see ‘‘tree visualization’’ in the methods).

Article Snippet: Pearson correlation and R squared between predicted and true log re uncertainty (i.e., standard deviation of the prediction, indicated by the error bars) a (see also Figures S3–S5). (C) Experimental validation of the top eight ranked compounds predicted by th chemical toward the EV71 ATCC VR-1432 strain.

Techniques: Activity Assay, Generated

Journal: Cell Reports Physical Science

Article Title: Antiviral discovery using sparse datasets by integrating experiments, molecular simulations, and machine learning

doi: 10.1016/j.xcrp.2025.102554

Figure Lengend Snippet: Figure 3. Impact of protonation states, urea, and OH—ions on structural dynamics and cross-linking in the EV71 pentamer (A–C) (A) SASA values for each residue and the relative changes in RMSF in the a-carbon among the protomer C of the EV71 pentamer, evaluating different protonation states with 2 wt % urea and without urea across a range of pH values. The purple stars denote ‘‘stable-bound’’ urea with RMSD less than 5 A˚ during the simulation and proximity to the residue of less than 6 A˚ . The results of all five protomers in the EV71 pentamer are in Figure S17. Significant differences in RMSF and stable-bound urea are mainly observed in (B) the hydrophobic pocket in VP1 and (C) the VP1-VP2 interface. (D) Relative changes in the fraction of native contacts between VP1 and VP2 in the EV71 pentamer, evaluating the protonation state at neutral pH with 2 wt % urea and without urea during the simulation time. The solid line represents a smoothed moving average, computed over a 2 ns window, to enhance clarity in the data trend. (E) Heatmaps depicting the quantity and stabilization of OH ions in proximity to various residues.

Article Snippet: Pearson correlation and R squared between predicted and true log re uncertainty (i.e., standard deviation of the prediction, indicated by the error bars) a (see also Figures S3–S5). (C) Experimental validation of the top eight ranked compounds predicted by th chemical toward the EV71 ATCC VR-1432 strain.

Techniques: Residue