Web-services

Many WHAT IF options are also available as Web services. If you don't know the difference between a web-server and a Web service, you don't need this page and you can click here.

All WHAT IF Web services are available for use through the SOAP protocol and through the REST protocol. The WSDL is available at http://wiws.cmbi.umcn.nl/wsdl/. I use the REST version only for test purposes, but they are operational and can be called using: http://wiws.cmbi.umcn.nl/rest/Web-service-name/id/4-letter-PDB-identifier/ so, for example, to calculate the solvent accessible surface of all atoms in 1crn you can use: http://wiws.cmbi.umcn.nl/rest/AtomAccessibilitySolvent/id/1crn/

Availability of Web services

This information is available as a separate page that will be updated each time a new Web service is added. We will also, from time to time, improve the documentation of the Web services. Improved Web services will get a new name that is similar to the old one, existing Web services will stay alive unaltered.

Choice of WHAT IF parameters

Web services do not leave much room for interactive parameter setting, and WHAT IF is principally a highly interactive program. So, I had to do something about defaults. In principle, if you know WHAT IF a bit, you should be able to easily gamble the parameters I selected, because those are the ones that you would get by not entering anything, and just hitting Enter in the interactive WHAT IF version.

Input to the Web services

All WHAT IF Web services take standard PDB files as input. These PDB files should preferably be in the 2008 remediated format, but most of the older file formats will probably be treated correctly also.

Sample scripts

A series of sample scripts can be found in the sample script tar-file. You can extract this archive from the command-line using the command:

tar xzf what-if-web-service-sample-scripts.tgz which generates the directory what-if-web-service-sample-scripts and in this diretory you can find a README and several sample scripts.

A small sample of the meta-file that is used by wiwsd to produce the WHAT IF Web services is available.

Rules for usage

We have put-up 8 chips for now, to service these Web services. If they get popular, we have the funds to buy more machines (at least if the users faithfully refer to the article about these services).

Still, feel free to use the Web services, but please stick to some rules:

  1. Do a test-run with a few files before sending a thousand or more.
  2. Run the Web services during (your) day-time so you can baby-sit the big runs a bit.
  3. If you run more than one Web service, then please send the next request only after the previous request gave a response.
  4. If you intend to call our Web services from software you distribute, or from web-servers or Web services you make publicly available, please tell us about that (not that there are restrictions or so, we are just curious about who are our users; and pehaps we can help).
  5. If you use the Web services, please refer to our article(s), i.e. refer to Nucleic Acids Res. 2010 May 25.
    WIWS: a protein structure bioinformatics Web service collection. PDF
    Hekkelman ML, Te Beek TA, Pettifer SR, Thorne D, Attwood TK, Vriend G.
    and to the article that comes closest to the option you used.
  6. If you find errors, report them!

Worked-out examples

The table below lists a series of Web services, the corresponding command to interactively run them using REST mode, and the output that that Web service will produce. In some cases the "expected result" contains blank lines. These are put in by my editor, and do not occur in the actual XML that you receive from the Web service.
Some nomenclature: "Things" that can form chains (amino acids, nucleotides, and sugars with the correct name) are called residues. Everything else is called ion (only single atomic things are called ion; muti-atomic things are called drug/ligand), water, or drug/ligand (drug and ligand tend to be used a bit random throughout the entire WHAT IF kingdom, sorry). So, metabolites, inhibitors, lipids, multi-atomic ions, and any unknown multi-atomic thing are called drug or ligand.