Applications¶
TODO: need current applications of actual rpxdock and maybe rifdock The concepts described here also apply to the rifdock project. The MatDes docking methodology, sicdock, “Motif Designer” and “Motif Docking” in use in the Baker Lab amount to early prototypes of rpxdock.
Two Sided Design (easy)¶
Cage Design¶
Neil, Jacob, Yang Very early versions used in the Science and Nature papers, “motif docking” used in latest icosahedron set and Jacob seems to think it was an improvement.
Cyclic Oligomer Design¶
Jorge: seems to be working fairly well, and with a very limited scaffold set.
Jeremy: 1 of 3 designs seems to work very well
Lattice Design¶
Ariel, soon to go to science or nature
Heterodimer Design¶
Daniel says it’s fantastic and many of his hetero-dimer designs may work. we’ll see if they’re specific.
One-sided Binder design (hard)¶
RIFdock¶
works well, see Jiayi’s HBI binder paper in nature, all the IPD work on protien and small molecule binders in the past 2-3 years is rifdock??
MotifDock¶
needs replacing with a rpxdock protocol!!
Aaron says it works well and is using it. Luke, Kenwuan and David La have used it and said it was helpful, but I dunno if they’re still using it.
Structure Prediction (0-sided, very hard)¶
no data, need to do benchmarks!