CABS-dock tutorial

1. Submitting new job
 1.1 Required input
 1.2 Advanced options
2. Interpreting job status
3. Interpreting results data
 3.1 Docking predictions results tab
 3.2 Clustering details tab
 3.3 Contact maps tab
 3.4 Download all files
 3.5 Reconstruction to all-atom representation and local optimization
 3.6 Viewing structures and simulation trajectory in Pymol
 3.7 Results visualization in VMD and gnuplot
4. Resubmiting job – excluding binding modes from previous runs
5. Example results page
6. Running CABS-dock from command line or scripts
 6.1 Submitting job
 6.2 Get job status
 6.3 Get job results
 6.4 Examples

1. Submitting new job

1.1 Required input

See an example screenshot of the “Submit new job” form on the right:

The only required data is protein structure and peptide sequence.

Protein receptor structure can be provided as file in the pdb format or protein pdb code along with the chain identifier(s), for example: 1RJK:A or 1CE1:HL (the structure is automatically obtained from Protein Data Bank database).

The following requirements apply to the input pdb files:
  • single or multi-chain proteins are accepted (chains must be up to 500 amino acids in length);
  • each residue in the provided pdb file should have a complete set of backbone atoms (i.e.: N, Cα, C and O);
  • side chain atoms may be missing.
  • non-standard amino acids are automatically changed to their standard counterparts.

Peptide sequence should be entered in single-letter amino acid code. Allowed size of the peptide is 3-30 amino acids.

After providing protein structure and peptide sequence, you can simply run simulation by clicking “Submit” button. However, it is possible to set some more parameters in “Optional” tab (see below for more details).

1.2 Advanced options

In “optional” settings tab you can:

  • specify project name, for better organization of your work: project names appear in the queue page.
  • provide your e-mail address, so we can inform you about your job status
  • mark "unlikely to bind regions" option to allow for the higher flexibility of selected receptor fragments (see 1.2.2 subsection form more details)
  • mark "flexible regions" option to select receptor residues that are unlikely to interact with the peptide (see 1.2.1 subsection form more details)
  • increase simulation length. You may increase the default (50) number of Monte Carlo macrocycles to be performed (the maximum number is 200). Increasing this number may be beneficial in more difficult modeling cases (e.g. for large receptor structures or for long peptides of more than 20 residues).
    An alternative way for dealing with such more demanding cases is to run independent simulation runs, and to analyze the results jointly.
  • define peptide secondary structure (if not, the psipred method is automatically used). The secondary structure should be defined for each residue in a three letter code: H, a helix; E, an extended state (beta sheet); and C, a coil (less regular structures).
    Note that overpredictions of the regular secondary structure (H or E) are more dangerous for the quality of the results than underpredictions (i.e. for residues with ambiguous secondary structure prediction assignment it is better to assign coil (C) than the regular (H or E) structure).

1.2.1 Selecting flexible regions

See an example

If “Mark flexible regions” is checked, after clicking “submit button” you will be redirected to the panel shown below:


The panel enables removing distance restraints that keep the receptor structure in a near native conformation For each selected residue, the user may choose from two preset settings: moderate or full flexibility.

Step by step instruction:
  • Select fragments by clicking amino acid symbols in the sequence
  • Use Ctrl with mouse to select second region of chain (on the sequence) to increase flexibility
  • After selecting proper regions, click Add region button
  • Select flexibility level (default is none, i.e. fully flexible, unconstrained fragment).
  • You can bookmark this page to postpone flexible regions selection. Do not forget to press save regions definition if you made some changes
  • When finish, just click Go to the next step! to send job to computational server.

1.2.2 Selecting unlikely to bind regions

See an example

If “Mark unlikely to bind regions” is checked you will be redirected to the panel which is similar to one described in the previous subsection:


Here you can select receptor residues that are unlikely to interact with the peptide to exclude some binding modes from the results.

Step by step instruction:
  • Select fragments by clicking amino acid symbols in the sequence
  • Use Ctrl with mouse to select second region of chain (on the sequence) to use multiple selection
  • After selecting proper regions, click Add region button
  • You can bookmark this page to postpone flexible regions selection. Do not forget to press save regions definition if you made some changes
  • When finish, just click Go to the next step! to send job to computational server.
Note that the information about selected “Unlikely to bind regions” will be available from the Project information tab.

1.2.3 Submitting contact information

To submit a docking task with the contact information, provide the restraint definition in the newly added "contact information" field using the following format:

residID:chainID  residID:chainID  cut-off  weight

  • residID is the residue number as in the input PDB file (i.e. 123)
  • chainID it the chain identificator (i.e. A; for peptide use "PEP"
  • cut-off is the maximal expected distance between the centers of mass of the restrained side-chains (default value: 5.0 Angstroms)
  • weight  is a weighting factor for penalty if distance is above cut-off (default value: 1.0)
For example, to introduce a restraint with cut-off distance 5.0 A and the restraint weight equal to 1.0 on residue 1060 of chain C and residue 6 of the peptide, type into the "contact inforation" field:

1060:C 6:PEP 5.0 1.0

To introduce multiple restraints, use multiple lines in the "contact information" field. For example, to use the previous restraint together with a second one, imposed on the residue 1066 of chain C and the residue 7 of the peptide (using the same parameters), type the following two lines in the "contact information" field:

1060:C 6:PEP 5.0 1.0
1066:C 7:PEP 5.0 1.0

If the parameters are omitted, the default values will be used. This way all the following three commands will result in the same docking settings:

1060:C 6:PEP 5.0 1.0
1060:C 6:PEP 5.0
1060:C 6:PEP

Note that contact information used in the docking will be provided under the"Project information" tab available from the unique job page.


1.2.4 Simulation time

Due to the fact that CABS-dock runs on our Department cluster, sometimes jobs performs slower (they waiting for free resources, with status in queue). Plot below presents averaged time (in hours) and min/max times for currently submitted jobs in a function of system (receptor + ligand) size, normalized by default number of simulation cycles (50).

2. Interpreting job status

After clicking the Submit button, you will be redirected to project information page.

If you have chosen “Do not show my job on the queue page” it is important to save the link to your job, otherwise your job will be accessible from the queue page. Under the unique link to your job you’ll find the job status updates and finally the job results.

The job status information will start from the job pending status:

followed by the running status:

The job ends with the done status, and additional tabs containing results are provided:

3. Interpreting results data

3.1 Docking predictions results tab



The left panel of the "Docking prediction results" contains visualization of the predicted complex (the peptide is shown in red). You can easily rotate and zoom the model using mouse. If the model is not displayed, please check if Web Graphics Library (webGL) is enabled in your browser (see the WebGL test page for more details). Alternatively, you can switch to JSmol which is an HTML5 JavaScript-only web app.

The right panel contains list of the resulting models. They are derived from the modeling trajectory by means of hierarchical clustering method – all models from the trajectory are divided into 10 groups (clusters) of similar structures. For each of the cluster one representative model is selected. Models are then ranked according to density of the clusters (model_1 represents the most dense cluster) and reconstructed to all-atom representation.

When you enter results page, model_1 (from the most dense cluster) is shown. To view other models click "View" button. You can also download models as pdb files by clicking "Download".

3.2 Clustering details tab

Under the “Clustering details” tab (see the screenshot below) you are provided with thorough insight into structural clustering data.


An interactive chart shows the composition of clusters of models vs. their trajectory affiliation. By clicking on the points representing models in the chart, you may view in 3D and download particular models in the pdb format.

The tab also contains a table summarizing basic information on clusters:

  • Cluster id and its medoid - the model which average dissimilarity to all models in a cluster is minimal). Files can be downloaded in pdb format.
  • Cluster density values (number of elements divided by average cluster rmsd>)
  • Average rmsd (average pairwise Cα rmsd value between models grouped in a cluster)
  • Max rmsd (maximum pairwise Cα rmsd value between models grouped in a cluster)
  • Number of elements (number of models grouped in a cluster)
  • Average cluster rmsd (average pairwise Cα rmsd value between models grouped in a cluster)

3.3 Contact maps tab

The “Contact maps” tab allows to investigate the interaction interface between the peptide and the receptor. An interactive chart shows a contact map between the peptide and the receptor residues. You may define the value of the contact cutoff distance i.e. distance between the closest heavy atoms of the residues (default value is 4.5 Å). At the bottom of the page a text list of the contacts shown on the maps.



3.4 Download all files

From “Docking predictions results” tab, you may download a compressed archive with the output data. The archive file contains the following data:

  • model_*.pdb - 10 final models (in the PDB format and all-atom representation)
  • cluster_*.pdb - cluster models (groups of models that have been classified in structural clustering to particular clusters; in the PDB format and C-alpha representation) Cluster numbering correspond to models numbering i.e. model_7.pdb is a representative model of models grouped in the seventh (ranked as seventh) cluster (cluster_7.pdb).
  • trajectory_*.pdb - complete trajectories (in the PDB format and C-alpha representation)
  • top1000.pdb - top 1000 models (in the PDB format and C-alpha representation)
  • input.pdb - the input structure of the receptor
  • README - a log file with all information to recreate the simulation
  • energy.txt - log file from the simulation with energy and its distribution; the columns contain the following data:
    • trajectory (replica) index
    • trajectory (replica) frame index
    • temperature (the parameter in the CABS model controlling the acceptance of new conformations – based on Monte Carlo method)
    • energy for protein receptor only (from CABS model)
    • energy for peptide only (from CABS model)
    • protein-peptide interaction energy (from CABS model)
    • protein-peptide total energy (from CABS model)

3.5 Reconstruction to all-atom representation and local optimization

For 10 final models, the CABS-dock server provides automated reconstruction to all-atom representation and local optimization using Modeller procedure (the optimization is done by the minimization with the DOPE, Discreet Optimized Protein Energy, statistical potential). Larger sets of CABS-dock models (1000 or 10,000, downloaded from the server) can be reconstructed by a user using standalone Modeller package.

The script for the Modeller reconstruction and optimization procedure is available here .

3.6 Viewing structures and simulation trajectory in Pymol

All downloadable pdb files (models, clusters, and trajectories available from the ‘Docking predictions results’ tab) can be easily viewed using molecular visualization software, like Pymol.

Clusters and trajectories contains only Cα atoms. In order to view Cα trace load the pdb file into Pymol and type:

show ribbon
set ribbon_trace_atoms, 1

You may also view multi-model files such as the simulation trajectories and cluster files. To do so load the pdb file into Pymol and type: 
show ribbon
set ribbon_trace_atoms, 1
mplay
If you want to view all models at ones type: 
set all_states, 1

See an example movie prepared in Pymol:

3.7 Results visualization in VMD and gnuplot

Here you can download a tutorial, which describes how to:
  • load all the necessary files into the VMD molecular graphics program
  • create simple graphic representations for viewing trajectories
  • align models from trajectories with a known receptor structure
  • calculate peptide RMSDs (root mean square deviation from the reference structure)
  • create plots from calculated RMSDs vs. energies from the CABS-dock results
Download tutorial [PDF]

4. Resubmiting job – excluding binding modes from previous runs

You may resubmit your job with changed job parameters. To do so go to the “Project information” tab and press Re-submit project.


You will be redirected to resubmission panel where you may define “optional settings” (see section 1.2). You may also select models (binding modes) to be excluded from future results. Technically, receptor residues making the most persistent contacts in the selected binding mode will be excluded from making favorite interactions with the peptide. In order to start computations click re-submit button.

5. Example results page

An example result page can be accessed here. See also an "Examples" section

6. Running CABS-dock from command line or scripts (RESTFull)

CABS-dock webserver may be operated throught RESTful services, using following URIs:

  • https://biocomp.chem.uw.edu.pl/CABSdock/REST/status/somejobidentifier check job status only
  • https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_info/somejobidentifier check information about submitted job
  • https://biocomp.chem.uw.edu.pl/CABSdock/REST/add_job/ submit new job
      Required json-formatted parameters:
    • receptor_pdb_code PDB code of receptor with or without chain info
      • OR receptor_file Send your PDB file with receptor
    • ligand_seq Ligand sequence
      Optional json-formatted parameters:
    • project_name project name
    • email email (info about job will be send to this email)
    • ligand_ss Ligand secondary structure
    • simulation_cycles Number of simulation cycles (max 200)
    • show_job ("True" or "False") if False - do not show job on the queue page
    • excluded_regions Array of excluded regions. You can select receptor residues that are unlikely to interact with the peptide.(start position, end position, chain)
    • flexible_regions Array of flexible regions (removing distance restraints that keep the receptor structure in a near native conformation). (start position, end position, chain, flexibility (full / moderate))
  • https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_results_all/somejobidentifier Get full results for job. Optional filter for attribute (min/max/range)
      • Optional json-formatted parameters:
    • value Attribute
    • min Minimal value
    • max Maximum value
      Parameters:
    • densitycluster density
    • rmsd Average RMSD
    • maxrmsd Max RMSD
    • counts Number of elements
  • https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_results/somejobidentifier Get results for job (most interesting informations). Optional filter for attribute (min/max/range)
      • Optional json-formatted parameters:
    • value Attribute
    • min Minimal value
    • max Maximum value
      Parameters:
    • densitycluster density
    • rmsd Average RMSD
    • maxrmsd Max RMSD
    • counts Number of elements
  • https://biocomp.chem.uw.edu.pl/CABSdock/REST/get_cluster/somejobidentifier/cluster_number Get cluster results.
  • https://biocomp.chem.uw.edu.pl/CABSdock/REST/get_trajectory/somejobidentifier/trajectory_number Get trajectory.
  • https://biocomp.chem.uw.edu.pl/CABSdock/REST/get_selected_trajectory/somejobidentifier/cluster_number/start/end Get selected part of trajectory. Start and end must be in the range (1,1000)

6.1 Submitting job


6.1.1 Submitting job from the command line with PDB code

Submit job for XYZ protein and SFDG ligand sequence, using cURL, with default parameters :
curl -H "Content-Type: application/json" -X POST -d '{"receptor_pdb_code":"XYZ", "ligand_seq":"SFGD"}' https://biocomp.chem.uw.edu.pl/CABSdock/REST/add_job/.

User should get output like: 

HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 30
Server: Werkzeug/0.10.4 Python/2.7.6
Date: Wed, 20 Jul 2015 19:53:23 GMT

{
  "jid": "a6433216640dcb3"
}
where jid is job identifier assigned to the just submitted job. Otherwise (for example if pdbcode doesn't exists or input data doesn't fullfill requirements), user should get output similar to: 
HTTP/1.0 404 NOT FOUND
Content-Type: text/html; charset=utf-8
Content-Length: 5521
Server: Werkzeug/0.9.6 Python/2.7.8
Date: Wed, 12 Nov 2014 13:56:48 GMT
[...]
or raise error 
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 165
Server: Werkzeug/0.10.4 Python/2.7.6
Date: Wed, 22 Jul 2015 20:02:41 GMT

{
  "error": "Protein code must be 4-letter (2PCY) or >5 letters (2PCY:A or 2PCY:AB ...)"
}

To override default parameters, user may post additional options, i.e.: curl -H "Content-Type: application/json" -X POST -d '{"receptor_pdb_code":"2IV9", "ligand_seq":"SFGD","project_name":"my_project1", "email":"mail@host.com", "ligand_ss":"CCHHC", "simulation_cycles":"100", "show_job":True, "excluded_regions":[{"start":"100","end":"340","chain":"A"}], "flexible_regions":[{"start":"101","end":"202","chain":"B","flexibility":"full"}]}' https://biocomp.chem.uw.edu.pl/CABSdock/REST/add_job/

6.1.2 Submitting job from the command line with PDB file

curl -X POST -F data='{"ligand_seq":"SFGDDD","email":"mail@host.com","show":"False", "excluded_regions":[{"start":"100","end":"340","chain":"A"}], "flexible_regions":[{"start":"800","end":"808","chain":"B","flexibility":"full"},{"start":"707","end":"777","chain":"A","flexibility":"moderate"}]}' -F file=@your_pdb_file.pdb https://biocomp.chem.uw.edu.pl/CABSdock/REST/add_job/

6.1.3 Submitting job from the Python script

import requests
import json

url = 'https://biocomp.chem.uw.edu.pl/CABSdock/REST/add_job/'
files = {'file': open('your_PDB_file.pdb')} #or use PDB code in var data
data = {
    "receptor_pdb_code": "2IV9", #or use PDB file in var files
    "ligand_seq": "SFGD",
    "email": "mail@host.com",
    "show": True,
    "project_name":"my_project1",
    "excluded_regions":[
        {
            "start": "1000",
            "end": "2000",
            "chain": "A"
        }
    ],
    "flexible_regions":[
        {
            "start": "101",
            "end": "202",
            "chain": "A",
            "flexibility": "full"
        },
        {
            "start": "300",
            "end": "370",
            "chain": "B",
            "flexibility": "moderate"
        },
    ]
}

response = requests.post(url, files=files, data=data) #request with file
#response = requests.post(url, data=data) # request without file
print response.text

6.2 Get job status


6.2.1 Bash CURL

To get job status send
curl -I https://biocomp.chem.uw.edu.pl/CABSdock/REST/status/somejobidentifier 
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 22
Server: Werkzeug/0.10.4 Python/2.7.6
Date: Sun, 26 Jul 2015 10:31:35 GMT

{
  "status": "done"
}
    Possible task statuses :
  • done Job is done - results are ready
  • pending / running / pre_quere Job is in progress
  • error Job ID is faulty

6.2.2 Python script

import requests
import json

url = 'https://biocomp.chem.uw.edu.pl/CABSdock/REST/status/somejobidentifier'

response = requests.get(url)
print response.text

Get job status with additional informations


6.2.3 Bash CURL

To get job status with additional informations send
curl -I https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_info/somejobidentifier 
HTTP/1.0 200 OK
Content-Type: application/json
Content-Length: 929
Server: Werkzeug/0.10.4 Python/2.7.6
Date: Sun, 26 Jul 2015 11:06:21 GMT

{
  "del": "Mon, 26 Oct 2015 19:11:32 GMT",
  "excluded": [
    "783:A - 937:A"
  ],
  "flexible": [
    "767:A - 937:A"
  ],
  "ligand_chain": "A",
  "ligand_sequence": "SFGDGFADF",
  "ligand_ss": "CCCCHHHHC",
  "project_name": "Docking project",
  "receptor_sequence": "MAPGGYVAPKAVWLPAVKAKGLEISSGTFTHRQGHIYMEEMNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVV",
  "ss_psipred": 0,
  "status": "pending",
  "status_change": "Sun, 28 Jun 2015 19:11:32 GMT",
  "status_date": "Sun, 28 Jun 2015 19:11:32 GMT"
}

6.2.4 Python script

import requests
import json

url = 'https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_info/somejobidentifier'

response = requests.get(url)
print response.text

6.3 Get job results


6.3.1 Get essential informations

    Essential informations for each model included:
  • Average RMSD
  • Max RMSD
  • Cluster density
  • Number of elements
  • Model data
  • Informations about submitted data
If you need to get more informations, data see chapter 6.3.2 'Get all informations'

6.3.1.1 Bash Curl

To get result send
curl -i https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_results/somejobidentifier

We strongly recommend to send curl with compression
curl -i -H 'Accept-Encoding: gzip,deflate' https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_results/somejobidentifier

In result: 
{
  "models": [
    {
      "average_rmsd": "5.29163",
      "cluster_density": "18.8978",
      "elements": "100",
      "info": {
        "del": "Wed, 07 Oct 2015 21:34:27 GMT",
        "ligand_chain": "A",
        "ligand_sequence": "MGTEATEQVSWGHYSGDEEDAYSAEPLPEL",
        "ligand_ss": "CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC",
        "project_name": "87aeb5bf523d141",
        "receptor_sequence": "AILPIASSCCTEVSHHISRRLLERVNMCRIQRADGDCDLAAVILHVKRRRICVSPHNHTVKQWMKVQAAKKNGKGNVCHRKKHHGK",
        "ss_psipred": 1,
        "status": "done",
        "status_change": "Tue, 09 Jun 2015 23:00:30 GMT",
        "status_date": "Tue, 09 Jun 2015 21:34:27 GMT"
      },
      "jobid": "87aeb5bf523d141",
      "max_rmsd": "28.8464",
      "model": 1,
      "model_data": "REMARK   1 secondary structure assigned by stride \nREMARK   2 stride output converted by stride2pdb version 0.01\nHELIX    1   1 ARG X   19  GLU X   23  1                                   5\nHELIX    2   2 HIS X   58  ALA X   69  1 [[....................]]"
    },
    {
      "average_rmsd": "7.75161",
      "cluster_density": "16.5127",
      "elements": "128",
      "info": {
        "del": "Wed, 07 Oct 2015 21:34:27 GMT",
        "ligand_chain": "A",
        "ligand_sequence": "MGTEATEQVSWGHYSGDEEDAYSAEPLPEL",
        "ligand_ss": "CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC",
        "project_name": "87aeb5bf523d141",
        "receptor_sequence": "AILPIASSCCTEVSHHISRRLLERVNMCRIQRADGDCDLAAVILHVKRRRICVSPHNHTVKQWMKVQAAKKNGKGNVCHRKKHHGK",
        "ss_psipred": 1,
        "status": "done",
        "status_change": "Tue, 09 Jun 2015 23:00:30 GMT",
        "status_date": "Tue, 09 Jun 2015 21:34:27 GMT"
      },
      "jobid": "87aeb5bf523d141",
      "max_rmsd": "28.2751",
      "model": 2,
      "model_data": "REMARK   1 secondary structure assigned by stride \nREMARK   2 stride output converted by stride2pdb version 0.01\nHELIX    1   1 ARG X   19  LEU X   22  1                                   4\nHELIX    2   2 THR X   59  ALA X   69  1                                  11\nSHEET    1   1 1 MET X  27  CYS X  28  0\nSHEET    2   2 1 LEU X  44  HIS X  45  0\nSHE [[....................]] "
  },
  {},{},{},....,{}
}

To get filtered results
curl -i -X POST -d '{"filter":"density","min":"10","max":"20"}' https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_results/somejobidentifier


6.3.1.2 Python script
import requests
import json

url = 'https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_results/somejobidentifier'

#filtering is optional
data = {
	"value":"rmsd",
	"min":"5",
	"max":"12"
	}

response = requests.post(url,data=data)
print response.text

6.3.2 Get all informations

    All informations for each model included:
  • Average RMSD
  • Max RMSD
  • Cluster density
  • Number of elements
  • Model data
  • Informations about submitted data
    • and extra :
  • Cluster data - if you need only cluster data see chapter 6.3.3
If you need to get a trajectory data, see chapter 6.3.4

6.3.2.1 Bash Curl

To get result send
curl -i https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_results_all/somejobidentifier

We strongly recommend to send curl with compression
curl -i -H 'Accept-Encoding: gzip,deflate' https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_results_all/somejobidentifier

In result: 
{
  "models": [
    {
      "average_rmsd": "5.29163",
      "cluster_data": "MODEL      102\nATOM      1  CA  ALA X   3      -0.304  -0.446 -12.449  1.00  1.00           C\nATOM      2  CA  ILE X   4       2.456   1.179 -13.176  3.00  1.00           C\nATOM      3  [.....]",
      "cluster_density": "18.8978",
      "elements": "100",
      "info": {
        "del": "Wed, 07 Oct 2015 21:34:27 GMT",
        "ligand_chain": "A",
        "ligand_sequence": "MGTEATEQVSWGHYSGDEEDAYSAEPLPEL",
        "ligand_ss": "CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC",
        "project_name": "87aeb5bf523d141",
        "receptor_sequence": "AILPIASSCCTEVSHHISRRLLERVNMCRIQRADGDCDLAAVILHVKRRRICVSPHNHTVKQWMKVQAAKKNGKGNVCHRKKHHGK",
        "ss_psipred": 1,
        "status": "done",
        "status_change": "Tue, 09 Jun 2015 23:00:30 GMT",
        "status_date": "Tue, 09 Jun 2015 21:34:27 GMT"
      },
      "jobid": "87aeb5bf523d141",
      "max_rmsd": "28.8464",
      "model": 1,
      "model_data": "REMARK   1 secondary structure assigned by stride \nREMARK   2 stride output converted by stride2pdb version 0.01\nHELIX    1   1 ARG X   19  GLU X   23  1",
      "trajectory_data": "MODEL        1\nREMARK CABSDock Temp 6.45\nREMARK CABSDock Erec -29.49\nREMARK CABSDock Elig -29.39\nREMARK CABSDock Eint 0.00\nREMARK CABSDock Etot -58.88\nATOM      1  CA  ALA X   3      -1.057"
    },
    {},{},{},....,{}
}

To get filtered results
curl -i -X POST -d '{"filter":"rmsd","min":"5","max":"12"}' https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_results_all/somejobidentifier


6.3.2.2 Python
import requests
import json

url = 'https://biocomp.chem.uw.edu.pl/CABSdock/REST/job_results_all/somejobidentifier'
#filtering is optional
data = {
	"value":"rmsd",
	"min":"5",
	"max":"12"
	}

response = requests.get(url,data=data)
print response.text

6.3.3 Get cluster


6.3.3.1 Bash Curl

To get cluster send
curl -i https://biocomp.chem.uw.edu.pl/CABSdock/REST/get_cluster/somejobidentifier/clusterNumber
where clusterNumber is number between [1,10] corresponding to model number.

We strongly recommend to send curl with compression
curl -i -H 'Accept-Encoding: gzip,deflate' https://biocomp.chem.uw.edu.pl/CABSdock/REST/get_cluster/somejobidentifier/clusterNumber

In result we get cluster data and informations about cluster: 
{
  "model": [
    {
      "average_rmsd": "8.45027",
      "cluster_data": "MODEL      101\nATOM      1  CA  LEU A   6      28.654  -0.817  25.718  1.00  1.00           C\nATOM      2  CA  GLY A   7      31.720  -3.251  26.268  3.00  1.00 [.......]",
      "cluster_density": "29.3482",
      "elements": "248",
      "jobid": "8ae372b8e877be4",
      "max_rmsd": "41.6541"
    }
  ]
}

6.3.4 Get trajectory


6.3.4.1 Bash Curl

To get trajectory send
curl -i https://biocomp.chem.uw.edu.pl/CABSdock/REST/get_trajectory/somejobidentifier/modelNumber
where modelNumber is between [1,10]

We strongly recommend to send curl with compression
curl -i -H 'Accept-Encoding: gzip,deflate' https://biocomp.chem.uw.edu.pl/CABSdock/REST/get_trajectory/somejobidentifier/modelNumber

In result we get trajectory data: 
{
  "model": [
    {
      "jobid": "8ae372b8e877be4",
      "trajectory": "MODEL        1\nREMARK CABSDock Temp 6.45\nREMARK CABSDock Erec -1529.95\nREMARK CABSDock Elig -7.95\nREMARK CABSDock Eint 0.00\nREMARK CABSDock Etot -1537.90\nATOM      1  CA  LEU A   6 [.........]"
    }
  ]
}

Additionally, you can take a section of the trajectory model
curl -i https://biocomp.chem.uw.edu.pl/CABSdock/REST/get_selected_trajectory/somejobidentifier/cluster_number/start/end



6.4 Examples


6.4.1 Example 1 (default settings)


The example with the default CABS-dock server settings using the following data:

  • Peptide sequence: SSRFESLFAG
  • Peptide secondary structure: CHHHHHHHHC
  • Receptor input structure: PDB ID: 2AM9, crystal structure of human androgen receptor in the unbound form

Bash CURL
curl -H "Content-Type: application/json" -X POST -d '{"receptor_pdb_code":"2AM9", "ligand_seq":"SSRFESLFAG", "ligand_ss":"CHHHHHHHHC"}' https://biocomp.chem.uw.edu.pl/CABSdock/REST/add_job/
Python script 
            import requests
import json

url = 'http://0.0.0.0:5000/REST/add_job/'
files = {'file': open('your_PDB_file.pdb')} #or use PDB code in var data
data = {
    "receptor_pdb_code": "2AM9"
    "ligand_seq": "SSRFESLFAG",
    "ligand_ss": "CHHHHHHHHC"
    response = requests.post(url, data=data)
    print response.text
}

response = requests.post(url, files=files, data=data) #request with file
#response = requests.post(url, data=data) # request without file
print response.text

6.4.2 Example 2 (increasing the flexibility of selected receptor fragments)


For each selected residue, the user may choose from two preset settings: moderate or full flexibility. Technically this is achieved by changing the default distance restrains (used to keep the receptor structure near to the input conformation). The assignment of moderate flexibility decreases the strength of restrains, while full flexibility assigned removes all the restraints imposed on the selected residue.


Example:

  • Peptide sequence: HPQFEK
  • Peptide secondary structure: CHHHCC
  • Receptor input structure: PDB ID: 2RTM, crystal structure of biotin binding protein in the unbound form

Using the CABS-dock “Mark flexible regions” option, we selected 10 residues (from 45th to 54th) forming the flexible loop and assigned the “fully flexible” setting to those residues.

Important : Must be used numbering of PDB format.

Bash CURL
curl -H "Content-Type: application/json" -X POST -d '{"receptor_pdb_code":"2RTM", "ligand_seq":"HPQFEK", "ligand_ss":"CHHHCC", "flexible_regions":[{"start":"45","end":"54","chain":"A","flexibility":"full"}]}' https://biocomp.chem.uw.edu.pl/CABSdock/REST/add_job/

Python script 
import requests
import json

url = 'http://0.0.0.0:5000/REST/add_job/'
files = {'file': open('your_PDB_file.pdb')} #or use PDB code in var data
data = {
    "receptor_pdb_code": "2RTM"
    "ligand_seq": "HPQFEK",
    "ligand_ss": "CHHHCC"
    "flexible_regions":[
        {
            "start": "45",
            "end": "54",
            "chain": "A",
            "flexibility": "full"
        }
    ]
    }
response = requests.post(url, data=data)
print response.text
}

response = requests.post(url, files=files, data=data) #request with file
#response = requests.post(url, data=data) # request without file
print response.text

6.4.3 Example 3 (excluding binding modes from docking search)


In the default mode, CABS-dock allows peptides to explore the entire receptor surface. However, in certain modeling cases it is known that some parts of the protein are not accessible (for example due to binding to other proteins) and therefore it could be useful to exclude these regions from the search procedure.


Example:

  • Peptide sequence: PQQATDD
  • Peptide secondary structure: CEECCCC
  • Receptor input structure: PDB ID: 1CZY:C, tumor necrosis factor receptor associated protein 2 in the unbound form

1CZY protein is a trimer and 1CZY:C makes the following contacts with 1CZY:A (according to http://ligin.weizmann.ac.il/cma/ server for analysis of protein-protein interfaces)


therefore listed above residues of C chain (the input protein) which are responsible for making contacts with A and B chains can be excluded from considering in the docking search.

Bash CURL
curl -H "Content-Type: application/json" -X POST -d '{"receptor_pdb_code":"1CZY:C", "ligand_seq":"PQQATDD", "ligand_ss":"CEECCCC", "excluded_regions":[ {"start":"334","end":"335","chain":"C"}, {"start":"338","end":"338","chain":"C"}, {"start":"341","end":"342","chain":"C"}, {"start":"345","end":"345","chain":"C"}, {"start":"350","end":"350","chain":"C"}, {"start":"385","end":"386","chain":"C"}, {"start":"416","end":"418","chain":"C"}, {"start":"420","end":"421","chain":"C"}, {"start":"458","end":"458","chain":"C"} ]}' https://biocomp.chem.uw.edu.pl/CABSdock/REST/add_job/

Python script 
import requests
import json

url = 'http://0.0.0.0:5000/REST/add_job/'
files = {'file': open('your_PDB_file.pdb')} #or use PDB code in var data
data = {
    "receptor_pdb_code": "1CZY:C"
    "ligand_seq": "PQQATDD",
    "ligand_ss": "CEECCCC"
    "excluded_regions":[
        {
            "start": "334",
            "end": "335",
            "chain": "C",
        },
        {
            "start": "338",
            "end": "338",
            "chain": "C",
        },
        {
            "start": "341",
            "end": "342",
            "chain": "C",
        },
        {
            "start": "345",
            "end": "345",
            "chain": "C",
        },
        {
            "start": "350",
            "end": "350",
            "chain": "C",
        },
        {
            "start": "385",
            "end": "386",
            "chain": "C",
        },
        {
            "start": "416",
            "end": "418",
            "chain": "C",
        },
        {
            "start": "420",
            "end": "421",
            "chain": "C",
        },
        {
            "start": "458",
            "end": "458",
            "chain": "C",
        }
    ]
    }
            
response = requests.post(url, data=data)
print response.text

Laboratory of Computational Biology, 2020