API - Documentation

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
For jobs successfully processed by ddmut, the following data will be returned:
  • 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
For jobs successfully processed by ddmut, the following data will be returned:
  • 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
For jobs successfully processed by ddmut, the following data will be returned:
  • 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
For jobs successfully processed by ddmut, the following data will be returned:
  • 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}

    }