Scatter Plot from Scientific Research

Structures generated by DiG resemble the diverse conformations of millisecond MD simulations. MD-simulated structures are projected onto the reduced space spanned by two time-lagged independent component analysis (TICA) coordinates (that is, independent component (IC) 1 and 2), and the probability densities are depicted using contour lines. Left: for the RBD protein, MD simulation reveals four highly populated regions in the 2D space spanned by TICA coordinates. DiG-generated structures are mapped to this 2D space (shown as orange dots), with a distribution reflected by the colour intensity. Under the distribution plot, structures generated by DiG (thin ribbons) are superposed on representative structures. AlphaFold-predicted structures (stars) are shown in the plot. Right: the results for the SARS-CoV-2 main protease, compared with MD simulation and AlphaFold prediction results. The contour map reveals three clusters, DiG-generated structures overlap with clusters II and III, whereas structures in cluster I are underrepresented.

DOI