Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
Fig 6
Intermediate results extracted from the “Molecular Interaction Potentials” workflow.
(a) Structural water molecules and ions placed in the energetically most favorable spots on the surface of the protein; (b) molecular interaction potential grids obtained from a positive probe (left, blue), a negative probe (middle, red), and a neutral probe (right, gray); and (c) potential energy (electrostatic + VdW) calculated for a protein–ligand interaction. The inline plot shows the representation of the protein residues with lower energy (higher affinity). (d) Representation of the residues contributing the most to the protein–protein complex interaction.