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.




Parameter Description Default value
BriX_hostname LoopX database hostname localhost
BriX_pass LoopX database password
BriX_port LoopX database port 3306
BriX_user LoopX database username
LoopX_database LoopX database name Astral95LoopBriX
LoopX_PDBDir Repository of the LoopX fragments(pdbs) ./
LR_chain Loop chain X
LR_dsspBegin DSSP information of the first anchor residue (H,B,E,G,I,T,S)
LR_dsspEnd DSSP information of the second anchor residue (H,B,E,G,I,T,S)
LR_nbrClassesToEvaluate Loop classes to evaluate 0
LR_pepEndRes Second anchor residue 0
LR_pepStartRes First anchor residue 0
LR_scop Loop scop family
LR_screenOuput Plots screen output 1
LR_sequence Loop sequence