Figure 1

MAVEN Interface Overview and Model Generation. A) Screenshot of MAVEN having completed an ANM model of the HIV-1 protease 1T3R using 198 alpha carbons and weighted springs. Motilities of each residue are shown; B-factors from the PDB file (blue) and mean squared fluctuations computed from the ENM (red). The correlation coefficient for these two curves is 0.70. B) Selecting by atom type within the Prepare Files module is shown with all atoms from 1T3R displayed. Methods to generate other coarse grained systems are provided and explained in the User's Manual including the average sugar and base position in nucleotides or C) residue or side chain centroid positions. D) Mixed resolution systems are also supported. We show the protease inhibitor in red and surrounding atoms as blue sticks with the rest of the structure coarse-grained to C^α atoms shown as green spheres. E) MAVEN has the unique ability to convert electron density maps into coarse-grained points. EMDB structure 1800 is shown as a density contour followed by an approximate surface filled with spherically coarse-grained points. All of these examples are given in greater detail in the User's Manual.