HotspotPred

Example Files
File HotspotPred.pdb Binary Data HotspotPred.cfg
Download and Copy HotspotPred.pdb and HotspotPred.cfg into your working directory and type:

./modelX -f HotspotPred.cfg

Or check the command line tab
Name Parameter Description Parameter Type Parameter Default
angle-dubiety Set allowed uncertainty for Phi Psi angles double 15.0
binder Molecule name of the binder/nanobody string *
CA-dubiety Set allowed uncertainty for CA-CA distance between triangles double 0.3
CB-dubiety Set allowed uncertainty for CB-CB distance between triangles double 1.0
dih-dubiety Dihedral angle dubiety double 10.0
scan-residues List of residues to explore (RA124,FA122) string *
target Molecule name of the target that we want to predict string *
Name Parameter Description Parameter Type Parameter Default Parameter Range
atom-type Atom type to be consider in the evaluation: BB,SC,ALL string BB 0-2
biassed Use biassed or non biassed forcefield bool false
command string
config Set a configuration file path
database-name Set the mySQL database name string PepXDB
database-pass Set the mySQL password string modelx
database-port Set the mySQL database port int 3306
database-server Set the mySQL server string localhost
database-user Set the mySQL username string modelx
excluded File with excluded pdb from queries path
help Show help screen
max-threads Set the maximum number of threads int 1
output-dir Set output directory path
output-file Get Pdb file without dna path noDna.pdb
pdb Set a PDB file path
pdb-dir Set PDB directory path
renumber Renumber the pdb bool false
./modelX --command=HotspotPred --pdb=HotspotPred.pdb --CA-dubiety=0.5 --CB-dubiety=0.4 --dih-dubiety=25 --angle-dubiety=25 --contacts-th=2 --target=B --binder=A --database-server=localhost --database-user=modelx --database-pass=modelx --database-name=PepXDB_20k > output.txt