LoopReconstruction is a new FoldX command that allows to graft loops from the LoopBriX database. In order to place the loops, the algorithm needs as input two anchor points, which have to be included in the LR_sequence parameter; e.g., if the sequence of the loop we want to model is AAAA and the anchor points are Y,Y then LR_sequence=YAAAAY. In order to facilitate the fitting of the loop on the anchors it is also necessary to provide the dssp info of the anchor points. The minimal configuration file for LoopReconstruction is:
command = LoopReconstruction pdb= LR.pdb LR_chain = A LR_pepStartRes = 338 LR_pepEndRes = 343 LR_screenOuput = 1 LR_sequence = YAAAAY LR_dsspBegin = H LR_dsspEnd = H LR_nbrClassesToEvaluate = 1 BriX_database = Whatif2650BriX BriX_PDBDir = Brix pdb fragments repository BriX_hostname = localhost BriX_user = "" BriX_pass = "" BriX_port = 3306 LoopX_database = Astral95 LoopX_PDBDir = Loopx pdb fragments repository
It can be run from the command line:
foldx4 --command=LoopReconstruction --pdb=LR.pdb --LR_chain=A --LR_pepStartRes=338 --LR_pepEndRes=343 --LR_screenOuput=1 --LR_sequence=YAAAAY --LR_dsspBegin=H --LR_dsspEnd=H --LR_nbrClassesToEvaluate=1 --BriX_database=Whatif2650BriX --BriX_PDBDir=Brix pdb fragments repository --BriX_hostname=localhost --BriX_user="" --BriX_pass="" --BriX_port=3306 --LoopX_database=Astral95 --LoopX_PDBDir=Loopx pdb fragments repository
After running LoopReconstruction you'll get the pdb models with the grafted loops. The models are numbered pdbId_loop_loopNum.pdb, where pdbId=1RA0_noLoop and loopNum is the fragment id identifying that loop in the LoopX database.
In order to run LoopReconstruction you need to install two extra fragment libraries: BriX and LoopBriX, available from the download page. The databases are composed of a MySQL dump and a directory with structures. Installation instructions can be found here.