Here we offer an API (Application Programming Interface) to assist users in integrating ddmut 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).
Single Prediction - http://biosig.lab.uq.edu.au/ddmut/api/prediction_single
POST - Job Submission
Arguments
- pdb_accession (optional) - 4 character PDB code
- pdb_file (optional) - file in PDB format
- chain (required) - Chain identifier
- mutation(required) - Point mutation code (aaFrom + residueNumber + aaTo)
- Reverse (optional) - Whether to predict reverse mutations (True/False). Default is False
- 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/ddmut/api/prediction_single -X POST -i -F pdb_file=@/home/ubuntu/1ba3.pdb -F mutation=H461D -F chain=A -F reverse=True
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2022 05:10:59 GMT
{
"job_id": "166495110391463"
}
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/ddmut/api/prediction_single -X GET -F job_id=166495110391463
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2022 05:10:59 GMT
{
"prediction": "-1.67",
"prediction_reverse": "1.016",
"chain": "A",
"res_number": 461,
"wild-type": "HIS",
"mutant": "ASP",
"results_page": "https://biosig.lab.uq.edu.au/ddmut/results_prediction/166495110391463",
}
List Prediction - http://biosig.lab.uq.edu.au/ddmut/api/prediction_list
POST - Job Submission
Arguments
- pdb_accession (optional) - 4 character PDB code
- pdb_file (optional) - file in PDB format
- mutation_list (required) - .txt or .csv file with mutation list. One mutation code per line (aaFrom + residueNumber + aaTo).
- Reverse (optional) - Whether to predict reverse mutations (True/False). Default is False
Return
- job_id - ID used for uniquely identify each job
Examples
-
curl
$ curl https://biosig.lab.uq.edu.au/ddmut/api/prediction_list -X POST -i -F pdb_file=@/home/ubuntu/1ag2.pdb -F mutations_list=@/home/ubuntu/mutations.txt
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2022 05:10:59 GMT
{
"job_id": "16649535589333909"
}
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/ddmut/api/prediction_list -X GET -F job_id=16649535589333909
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2022 06:11:53 GMT
{
"0": {"mutation":"Q217R","chain":"A","prediction":"-0.69"},
"1": {"mutation":"V180I","chain":"A","prediction":"-0.55"},
"2": {"mutation":"V210I","chain":"A","prediction":"-0.14"},
"3": {"mutation":"T190V","chain":"A","prediction":"0.33"},
}
Alanine Scanning - http://biosig.lab.uq.edu.au/ddmut/api/prediction_scanning
POST - Job Submission
Arguments
- pdb_accession (optional) - 4 character PDB code
- pdb_file (optional) - file in PDB format
Return
- job_id - ID used for uniquely identify each job
Examples
-
curl
$ curl https://biosig.lab.uq.edu.au/ddmut/api/prediction_scanning -X POST -i -F pdb_file=@/home/ubuntu/1ag2.pdb
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2022 05:10:59 GMT
{
"job_id": "16705716575422666"
}
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/ddmut/api/prediction_scanning -X GET -F job_id=16705716575422666
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2022 06:11:53 GMT
{
"0": {"mutation":"G124A","chain":"A","prediction":"-0.18"},
"1": {"mutation":"L125A","chain":"A","prediction":"-1.22"},
...,
"104": {"mutation":"Y226A","chain":"A","prediction":"-1.75"},
}
Multiple Mutations Prediction - http://biosig.lab.uq.edu.au/ddmut/api/prediction_mm
POST - Job Submission
Arguments
- pdb_accession (optional) - 4 character PDB code
- pdb_file (optional) - file in PDB format
- mutation_list (required) - .txt or .csv file with mutation list. One mutation code per line (aaFrom + residueNumber + aaTo).
- Reverse (optional) - Whether to predict reverse mutations (True/False). Default is False
Return
- job_id - ID used for uniquely identify each job
Examples
-
curl
$ curl https://biosig.lab.uq.edu.au/ddmut/api/prediction_mm -X POST -i -F pdb_file=@/home/ubuntu/2rn2.pdb -F mutations_list=@/home/ubuntu/mutations.txt
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2022 05:10:59 GMT
{
"job_id": "16705686765979645"
}
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/ddmut/api/prediction_mm -X GET -F job_id=16705686765979645
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2022 06:16:53 GMT
{
"A H62P;A T40A;A K122R": {"prediction": 0.45, "single_predictions": "0.43;-0.23;0.18", "sum_single_predictions": 0.38, "avg_distance": 29.67},
"A E119V;A K60R": {"prediction": 0.07, "single_predictions": "0.33;0.11", "sum_single_predictions": 0.46, "avg_distance": 22.12},
"A E119V;A R41C": {"prediction": 1.23, "single_predictions": "0.36;0.16", "sum_single_predictions": 0.51, "avg_distance": 28.61}
}