Docking (PADA1)

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

./modelX -f Docking.cfg

Or check the command line tab
Name Parameter Description Parameter Type Parameter Default Parameter Range
cbeta-angles Maximun allowed angle between CBs after X axis superimposition in degrees double 5 0-360
concordance-number Set the number of docks per peptide to consider them as a result int 1 1-100
deep-scan If a fragment is found recalculate energy using a full pep-threshold bool TRUE
discarded-list used to discard fragments from certain pdb ids path
dnax-length Set length of the digested dna fragments int 6 4-14
dock-length Set length of the digested dock fragments int 6 4-14
double-check If a fragment is found recalculate energy using a full pep-threshold bool TRUE
dubiety Set allowed uncertainty for the E2E dist double 0.1 0-1
energy-threshold Set the force field energy threshold per base pair double -0.1 0-100
fit-level CA fit level double 2 2-4
fit-threshold Threshold para peptide fit double 0.5 0-20
min-contacts Minimum number of residue contacts to consider a docking model int 2 1-10
mol Mol to scan with peptides string *
pep-mismatches Maximum number of mismatches for the scan peptide int 1 1;6
pep-threshold Maximum interaction distance around the anchor peptide, 18 is a good first choice double 18 0-500
pepx-length Set length of the digested peptide fragments int 6 6-12
quick-scan Performs a quick scan bool FALSE
residue Residue to scan with peptides int -100000
residue-begin Residue to scan with peptides int -100000
residue-end Residue to scan with peptides int -100000
sections Set circunference portions tu use as comparative rotation on X double 72 0-360
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=Docking --pdb=Docking.pdb --pep-mismatches=2 --dock-length=6 --pepx-length=6 --dubiety=0.1 --sections=72 --cbeta-angles=5 --mol=* --residue-begin=2 --residue-end=245 --fit-threshold=0.5 --fit-level=2 --min-contacts=2 --quick-scan=false --pep-threshold=18 --energy-threshold=-0.1 --atom-type=BB --deep-scan=true --double-check=true --database-name=DnaXDB --database-server=localhost --database-user=modelx --database-pass=modelx