An optional EC number to filter the list of motifs by
GET /motifs/{pdbid}
Get a specific motif
Path parameters
Parameter
Type
Function
pdbid
String
The unique PDB ID of the motif
GET /motifs/debug
TEMPORARY. Stores 4 hard-coded Motifs into the database
Ligands
GET /ligands/{ECNumber}
Get ligands associated with the specified EC
Path parameters
Parameter
Type
Function
ECNumber
String
The EC number you want ligands associated with
Docking
To perform docking, start by calling the POST /dock/dockligand endpoint.
Once you receive a 200 status and a job ID, continue to query the GET /dock/dockligand endpoint
Once you receive a 200 status, active site data, binding affinities and job ID, call GET /dock/retrievefile
Continue to call GET /dock/retrievefile until a 200 status is returned.
If you would like to receive the completed docked file again, you may call the GET /dock/retrievefile endpoint
The location of the AutoDock Vina and OpenBabel deployments may be configured in the application.properties file
Docking API
POST /dock/dockligand
Convert the supplied ligand and protein to pdbqt format using OpenBabel then start an AutoDock Vina job
Form Parameters
Parameter
Type
Function
macromolecule
File
Protein file for docking
ligand
File
Ligand file for docking
ligandID
String
Optional ligand ID. If ligand file is not provided, ligand ID will be used to download ligand from the PDB
macromoleculeID
String
Optional macromolecule ID. If macromolecule file is not provided, macromolecule ID will be used to download macromolecule from the PDB
center_x
number
Center of docking area in the x axis
center_y
number
Center of docking area in the y axis
center_z
number
Center of docking area in the z axis
size_x
number
Size of docking area in the x axis
size_y
number
Size of docking area in the y axis
size_z
number
Size of docking area in the z axis
Returns
200 OK - When job has been completed successfully
Field
Type
Function
jobId
String
ID of the AutoDock Vina job
macromolecule
String
Name of macromolecule file
ligand
String
Name of ligand file
GET /dock/dockligand
Checks the status of an AutoDock Vina job. When complete, sends docked ligand file to OpenBabel and returns a list of binding affinities and active sites.
For active site generation to function, ensure that the motif database has been generated.
Path Parameters
Parameter
Type
Function
jobId
String
ID of the AutoDock Vina job
pdbId
String
Id of protein for determination of active sites
Returns
200 OK - When job has completed successfully
203 - When job is still processing
Field
Type
Function
babelJobId
String
Job ID of OpenBabel file conversion
dockingData
array
List of binding affinities and free energy values
activeSites
array
List of active site data for protein
Docking Data
Each entry in the docking data array is in the format [model number, affinity, rmsd upper, rmsd lower]
Active Sites
Each entry in the active sites array takes the form:
Field
Type
Function
residueId
number
Id of active site residue in protein
residueChainName
String
Name of chain active site resides in
residueAltLoc
String
Alternate location of active site residue
GET /dock/retrievefile
Retrieves a completed job from OpenBabel
Path Parameters
Parameter
Type
Function
babelJobId
String
ID of the OpenBabel job
Returns
200 OK - When job has completed successfully
203 - When job is still processing
Requested completed pdb file
POST /dock/exportLigands
Converts the provided array of free energy values into a csv format
JSON Parameters
Parameter
Type
Function
ligands
array
List of ligands to export
Ligand
Parameter
Type
Function
name
String
name of ligand
bindingEnergy
number
Binding energy of ligand
modeNumber
number
Mode number of ligand
rmsdUpper
number
Upper bound of rmsd of ligand
rmsdLower
number
Lower bound of rmsd of ligand
Returns
200 OK
csv output file in the format Name,Mode Number,Binding Energy,RMSD Lower,RMSD Upper