Here we offer an API (Application Programming Interface) to assist users in integrating DynaMut2 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 - https://biosig.lab.uq.edu.au/dynamut2/api/prediction_single
POST - Job Submission
Arguments
- pdb (optional) - 4 character PDB code
- pdb_file (optional) - file in PDB format
- chain (required) - Chain identifier
- mutation(required) - Point mutation code (aaFrom + residueNumber + aaTo)
- 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/dynamut2/api/prediction_single -X POST -i -F pdb_file=@/home/ubuntu/1u46.pdb -F mutation=E346K -F chain=A
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2020 05:10:59 GMT
{
"job_id": "159176585954"
}
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/dynamut2/api/prediction_single -X GET -F job_id=15917658595
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2020 05:10:59 GMT
{
"prediction": "1.4",
"chain": "A",
"res_number": 346,
"wild-type": "E",
"mutant": "K",
"results_page": "https://biosig.lab.uq.edu.au/dynamut2/results_prediction/15917658595",
}
List Prediction - https://biosig.lab.uq.edu.au/dynamut2/api/prediction_list
POST - Job Submission
Arguments
- pdb (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).
Return
- job_id - ID used for uniquely identify each job
Examples
-
curl
$ curl https://biosig.lab.uq.edu.au/dynamut2/api/prediction_list -X POST -i -F pdb_file=@/home/ubuntu/1u46.pdb -F mutations_list=@/home/ubuntu/mutations.txt
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2020 05:10:59 GMT
{
"job_id": "159177158175"
}
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/dynamut2/api/prediction_list -X GET -F job_id=159177158175
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2020 06:11:53 GMT
{
"1": {"mutation":"E346K","chain":"A","prediction":"1.4"},
"2": {"mutation":"A347K","chain":"A","prediction":"1.7"},
"3": {"mutation":"A347Y","chain":"A","prediction":"0.23"},
}
Multiple Mutations Prediction - https://biosig.lab.uq.edu.au/dynamut2/api/prediction_mm
POST - Job Submission
Arguments
- pdb (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).
Return
- job_id - ID used for uniquely identify each job
Examples
-
curl
$ curl https://biosig.lab.uq.edu.au/dynamut2/api/prediction_mm -X POST -i -F pdb_file=@/home/ubuntu/1u46.pdb -F mutations_list=@/home/ubuntu/mutations.txt
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2020 05:10:59 GMT
{
"job_id": "159177154575"
}
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/dynamut2/api/prediction_mm -X GET -F job_id=159177154575
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 33
Date: Wed, 10 Jun 2020 06:16:53 GMT
{
"A E346K;A T118P": {"avg_distance":"47.18","prediction":"-0.84","sum_ddg":"-0.42"},
}