Here we offer an API (Application Programming Interface) to assist users in integrating mmCSM-PPI into their research pipelines.
In summary, all jobs submitted to our server are labelled with a unique ID which is used to query the status (in queue, processing, processed).
mmCSM-PPI allows for two distinct types of submissions, manual and systematic. Here we summarise the inputs and outputs for using the API for these two types of submissions
Manual - https://biosig.lab.uq.edu.au/mmcsm_ppi/api/manual
POST - Job Submission
Arguments
- pdb (optional) - 4 character PDB code
- pdb_file (optional) - file in PDB format
- mutations_list(required) - Upload a plain text file with one multiple mutation per line. Download sample
- email (optional) - Email for contact when the job is finished
Return
- job_id - ID used for uniquely identify each job
Examples
-
curl
$ curl https://biosig.lab.uq.edu.au/mmcsm_ppi/api/manual -X POST -i -F pdb_accession="1cse" -F mutations_list=@/home/ubuntu/mutations.txt
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Dec 2020 05:10:59 GMT
{
"job_id": "160706007808"
}
GET - Retrieve Job Results
Arguments
- job_id - ID used for uniquely identify each job. Generated upon submission
Return
For jobs still being processed or waiting on queue, the message below will be returned from querying this endpoint:- message - RUNNING
- prediction -
Examples
-
curl
$ curl https://biosig.lab.uq.edu.au/mmcsm_ppi/api/manual -X GET -F job_id=160706007808
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Dec 2020 05:13:29 GMT
{
"E Q2M; I R48A; E T33A": {
"average_distance": 22.14,
"individual_predictions": {
" E T33A": -0.71,
" I R48A": -0.72,
"E Q2M": -0.163
},
"prediction": -1.27
},
"I D46A; I R48A": {
"average_distance": 6.48,
"individual_predictions": {
" I R48A": -0.72,
"I D46A": -2.287
},
"prediction": -2.29
},
"I D46A; I R48A; E T33A": {
"average_distance": 11.29,
"individual_predictions": {
" E T33A": -0.71,
" I R48A": -0.72,
"I D46A": -2.287
},
"prediction": -2.89
},
"I D46A; I R48K": {
"average_distance": 6.48,
"individual_predictions": {
" I R48K": -0.806,
"I D46A": -2.287
},
"prediction": -2.27
}
}
Systematic - https://biosig.lab.uq.edu.au/mmcsm_ppi/api/systematic
POST - Job Submission
Arguments
- pdb (optional) - 4 character PDB code
- pdb_file (optional) - file in PDB format
- chain_id (required) - Chain identifier for systematic evaluation of interface.
- email (optional) - Email for contact when the job is finished
Return
- job_id - ID used for uniquely identify each job
Examples
-
curl
$ curl https://biosig.lab.uq.edu.au/mmcsm_ppi/api/systematic -X POST -i -F pdb_file=@/home/ubuntu/1cse.pdb -F chain_id="I"
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, Dec Jun 2020 03:11:09 GMT
{
"job_id": "160706129233"
}
GET - Retrieve Job Results
Arguments
- job_id - ID used for uniquely identify each job. Generated upon submission
Return
For jobs still being processed or waiting on queue, the message below will be returned from querying this endpoint:- message - RUNNING
- Array list of results (in json format) for each mutation identified with a sequencial identifying number
Examples
-
curl
$ curl https://biosig.lab.uq.edu.au/mmcsm_ppi/api/systematic -X GET -F job_id=160706129233
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, Dec Jun 2020 08:01:12 GMT
{
"I T44P;I D46G;I L45G": {
"avg_distance": 4.39,
"individual_predictions": {
"D46G": -2.057,
"L45G": -2.019,
"T44P": -3.271
},
"prediction": -5.98
},
"I T44P;I D46G;I V43P": {
"avg_distance": 6.2,
"individual_predictions": {
"D46G": -2.057,
"T44P": -3.271,
"V43P": -1.899
},
"prediction": -6.01
},
"I T44P;I D46P;I L45D": {
"avg_distance": 4.39,
"individual_predictions": {
"D46P": -2.838,
"L45D": -2.257,
"T44P": -3.271
},
"prediction": -6.07
},
"I T44P;I D46P;I L45E": {
"avg_distance": 4.39,
"individual_predictions": {
"D46P": -2.838,
"L45E": -1.892,
"T44P": -3.271
},
"prediction": -5.94
},
"I T44P;I D46P;I L45G": {
"avg_distance": 4.39,
"individual_predictions": {
"D46P": -2.838,
"L45G": -2.019,
"T44P": -3.271
},
"prediction": -5.93
},
"I T44P;I D46P;I V43P": {
"avg_distance": 6.2,
"individual_predictions": {
"D46P": -2.838,
"T44P": -3.271,
"V43P": -1.899
},
"prediction": -6.09
},
"I T44P;I D46V;I L45E": {
"avg_distance": 4.39,
"individual_predictions": {
"D46V": -1.992,
"L45E": -1.892,
"T44P": -3.271
},
"prediction": -5.94
},
"I T44P;I D46V;I V43P": {
"avg_distance": 6.2,
"individual_predictions": {
"D46V": -1.992,
"T44P": -3.271,
"V43P": -1.899
},
"prediction": -6.06
},
"I T44P;I L45D;I D46G": {
"avg_distance": 4.39,
"individual_predictions": {
"D46G": -2.057,
"L45D": -2.257,
"T44P": -3.271
},
"prediction": -6.04
},
}