Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock
Fig 2
Example inputs and docking output architectures currently supported by RPXDock.
X/Y/Z cartesian axes are shown in red, green, and blue respectively. Corresponding translational and rotational DOFs are sampled along and around these axes. Axes where DOFs are not sampled for an architecture are colored gray. A. Asymmetric docking samples 6 DOFs belonging to the first of two input monomers. B. Cyclic docking samples four DOFs belonging to an input monomer to generate a cyclic structure with its cyclic axis aligned to the Z axis. C-F. Oligomeric input structures must have their cyclic axis aligned to the Z axis and the input .pdb should only contain the asu (dark). Stacking, dihedral, polyhedral group, and wallpaper docking samples the rotational and translational DOF along the Z axis of the input cyclic oligomer, which is aligned during docking to the relevant rotational symmetry axes in the target architecture.