moltimate-backend

ProMol successor's backend application.

Contents

• Setup & Run
• Wiping Local Database
• API Summary
• API Details

Setup & Run

IntelliJ

To start the application from IntelliJ, import the project as a Maven project, and run the main(...) entrypoint in Application.java.

Maven CLI

To start the application using Maven's CLI, run:

    mvn spring-boot:run

Wiping Local Database

To wipe the database, delete the generated file moltimate.mv.db at the root of the project.

API Summary

This briefly summarizes all API endpoints.

Alignments

HTTP Method	Endpoint	Function
POST	/align/activesite	Aligns protein active sites with motifs

Motifs

HTTP Method	Endpoint	Function
GET	/motifs	Get a list of motifs
GET	/motifs/{pdbid}	Get a specific motif
GET	/motifs/debug	TEMPORARY. Stores 4 hard-coded Motifs into the database

Ligands

HTTP Method	Endpoint	Function
GET	/ligands/{ECNumber}	Get ligands associated with the specified EC

Docking

HTTP Method	Endpoint	Function
POST	/dock/dockligand	Begins AutoDock Vina job
GET	/dock/dockligand	Retrieves binding affinities and active sites, and starts final OpenBabel conversion
GET	/dock/retrievefile	Retrieves OpenBabel job
GET	/dock/exportLigands	Exports ligand data to csv format

API Details

This outlines every API's endpoints, request types, and expected request parameters or JSON payload.

Alignments

POST /align/activesite

Aligns protein active sites with motifs

Request body parameters

Parameter	Type	Function
pdbIds	String Array	The PDB IDs of the proteins that will be aligned with each motif
ecNumber	String	Filters the set of motifs. This can be partially-qualified ("3", ""3.4", "3.4.21", or "3.4.21.1")
options	String Array	NOT IMPLEMENTED. Additional options available for active site alignments
filters	String Array	NOT IMPLEMENTED. Additional ways to filter the set of motifs

Example JSON request

{
    "pdbIds": ["8gch", "1ezi", "1ma0"],
	"ecNumber": "3.4.21.1",
	"options": ["rmsd"],
	"filters": []
}

Motifs

GET /motifs

Get a list of motifs

Query string parameters

Parameter	Type	Function
ecnumber	String	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