3 replies [Last post]
beta_helix's picture
User offline. Last seen 3 hours 12 min ago. Offline
Joined: 05/09/2008
Groups: None

These were the Top 20 most-used recipes during CASP10:

Recipe Name / Number of times run on CASP10 puzzles

Reset / 8691
Rav3n_pl DRW v3.4 / 7003
Blue Fuse v1.1 / 6569
Rav3n_pl GAB v0.6 loss / 3863
Rav3n_pl Compressor v2.2 loss / 3826
Rav3n_pl Voids Killer v0.4 / 2475
Rav3n_pl Fuzes v1.2 / 2436
Rav3n_pl GAB v2.0.5 / 2292
Rav3n`s repeat Fuze / 2264
Rav3n_pl Hydro PulleR v2 / 1984
Quaking Rebuild V2 1.0 / 1859
Helix Curler 1.6.2 fuze fix / 1371
Loop rebuild 2.0 / 1302
QuakeR v3.0 / 1236
Rav3n_pl GAB v0.5 loss / 1220
Rav3n_pl DRW fast / 1216
gary Minima Finder v0.1 / 1148
Red Fuse / 1113
Zero Length Bands v 1.0.3 -- Brow42 / 1111
Rav3n_pl Total FuzeR v2.0.1 / 1111

After CASP9 we performed comparisons between the most popular recipes used by Foldit players and the Rosetta Relax protocol. This was published in the Foldit PNAS paper: tinyurl.com/foldit-PNAS

We'd like to run similar benchmarks this time around using many of the recipes listed above, but need your expertise to learn under what conditions each individual recipe performs best.

If you found a particular recipe to be most useful for particular circumstances (for example: when starting from a server refinement model or after threading an alignment) please send me a PM or feel free to post a comment below.

We thank you for your insights on this... and Happy New Year to you all!

marie_s's picture
User offline. Last seen 2 years 11 weeks ago. Offline
Joined: 05/18/2008
Groups: None
how I use them

most often in that order :

Rav3n_pl Fuzes v1.2 : all the time, after each manual move
Rav3n_pl DRW : after a big rebuild, to make the little rebuilds so almost all the time
QuakeR : almost never, I use almost always local quake and also quake shearing and quake slice instead because QuakeR tends to make protein round ; quake de novo at the start
Loop rebuild 2.0 : after some manual working and DRW, this recipe is the recipe for all night and day
Quaking Rebuild V2 1.0 : after DRW, loop rebuild and local quake. Very powerful so can put the protein in an abyssal local minima
Rav3n_pl GAB v2.0.5 : after the major work of rebuilders and quakes and before another run of them
Helix Curler 1.6.2 fuze fix : only for coil coiled
Rav3n_pl Compressor v2.2 loss : always at the very end, even after walking rebuild and LWS

Joined: 02/20/2013
Groups: None
hey

Usable info.
thanks

Joined: 11/17/2009
Groups: Russian team
Rav3n_pl GAB v2.0.5 and

Rav3n_pl GAB v2.0.5 and Rav3n_pl GAB BiS and also mine CM - Compressor in random modulation mode every time when other scripts cannot get any points.

Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons