Run a quick NERDSS simulation from a PDB with multiple chains.
These ioNERDSS hyperparameters control how your structure is turned into a NERDSS model. They apply to whichever option you submit above. Leave them unchanged to use the ioNERDSS defaults.
Contact search radius per atom pair when detecting interfaces. Larger values find more contacts between chains. Default: 0.6
Minimum number of contacting residues, on each chain, required to accept an interface. Larger values keep only substantial interfaces. Default: 3
Sequence identity threshold for treating two chains as repeats of the same molecule type (0.5 = 50% identity). Default: 0.5
NERDSS is a particle-based reaction-diffusion simulator. By modeling proteins as multi-site rigid bodies, NERDSS simulates self-assembly dynamics based on reaction rules and diffusion.
ionerdss simplifies the workflow by preparing NERDSS inputs from PDB files, running simulations, and analyzing results.
Please post to the discussion forum or create a GitHub issue to let us know.