HotspotPred
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=5bop_3_Repair.pdb CA-dubiety=0.5 CB-dubiety=0.4 dih-dubiety=25 angle-dubiety=25 contacts-th=2 target=B binder=A excluded=excluded.txt --database-server=localhost --database-user=modelx --database-pass=modelx -database-name=PepXDB_20k
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