Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
Fig 5
Markdown documentation and intermediate results extracted from the “Macromolecular Coarse-Grained Flexibility” workflow.
(a) Eigenvalue residue components analysis, indicating the residues contributing the most to the key essential deformations of the protein. An associated NGL widget displays these residues in ball and stick representation (red); (b) domain decomposition analysis displayed along the pseudo-trajectory with the simpletraj tool; (c) RMS inner product (RMSip) for all the CG pseudo-trajectories against an atomistic MD simulation; and (d) extract of documentation included for the NMA CG method.