Australian-Protein-Design-Initiative

Runs the nf-binder-design Nextflow pipeline for de novo protein binder design. Covers RFdiffusion (--method rfd), partial diffusion (--method rfd_partial), RFdiffusion3 (--method rfd3), BindCraft (--method bindcraft), Germinal (--method germinal), BoltzGen (--method boltzgen), Boltz Pulldown (--method boltz_pulldown), and FoldSeek (--method foldseek or --do_foldseek). Use when the user wants to design protein binders, nanobodies, or peptides, set up or run nf-binder-design, configure HPC/SLURM, or troubleshoot pipeline errors.