API - Documentation

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 - http://biosig.unimelb.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 http://biosig.unimelb.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"

    }

  • python launch

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 DynaMut2, the following data will be returned:
  • prediction -

Examples

  • curl

    $ curl http://biosig.unimelb.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": "http://biosig.unimelb.edu.au/dynamut2/results_prediction/15917658595",

    }

  • python launch

List Prediction - http://biosig.unimelb.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 http://biosig.unimelb.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"

    }

  • python launch

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 DynaMut2, 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 http://biosig.unimelb.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"},

    }

  • python launch

Multiple Mutations Prediction - http://biosig.unimelb.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 http://biosig.unimelb.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"

    }

  • python launch

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 DynaMut2, 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 http://biosig.unimelb.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"},

    }

  • python launch