WHAT IF servers help


The program WHAT IF provides nearly 2000 options in fields as diverse as homology modelling, drug docking, electrostatics calculations, structure validation and visualisation. This set of servers gives everybody access to some of these options.
If you want/need to run the same server over a very large set of PDB entries, please don't do that interactively, but use the web services (WSDL; HELP), or ask us to do it in batch mode. The going rate for such a service is about one good bottle of old single-malt whiskey per batch run per 5000 PDB files.


These servers are running on a reasonably fast server. We expect that even the most CPU intensive servers will return an answer in a few minutes for a PDB file that contains a few hundred residues. We ask you to refrain from using these servers for NMR ensembles. If you want to run a server on an NMR ensemble, submit only the representative model. Although WHAT IF can cope with NMR ensembles, these servers cannot in all cases because WHAT IF often needs to ask the user some additional information when working with NMR ensembles, and these servers do not allow for such interactions. After saying that, if you do have success, please feel free to tell us.
When you submit your PDB file to a server, the server will tell you that WHAT IF is running. Just wait a few minutes, and the result will come.

Input format information

Most servers take a PDB file as input. You can read everything about the PDB format at the site of the PDB. The homology modelling servers additionally require sequence files in PIR format. There is a special page with help available. There is some information available about how to address residues as server input. This information is found on a separate page.

Output format information

There is some information available about WHAT IF's ouput formats. This information is found on a separate page.


This new service is proving more and more popular. We have plans to increase capacity to meet demand, so feel free to make use of this. As of 2000, jobs are handled in parallel on a multi processor (SMP) server. We don't currently have any user restrictions, and hope to continue with this policy - by increasing our capability to serving results concurrently. We reserve the right to make restrictions should an individual abuse us - currently that would be by submitting say batches of 10 jobs at a time. This service is free of cost to academia and industry alike. Although industrial users will probably want more than our guarantee of security and confidentiality, we are willing to try to accommodate your needs in this area.

Server distribution

If you want these servers to work at your site, you can contact us. The software to generate more servers will upon request be distributed too.

Making your own servers

Guidelines for making your own servers are available. This boils down to building a server description block in the file WhatifServers.py and running the script HtmlFactory.py. It does not make sense to try to make your own servers if you don't understand WHAT IF. WHAT IF courses are given about once per year, normally in Nijmegen or in Heidelberg.


The servers are all generated by a server generation program that fully automatically converts server meta-information into a set of servers. The servers are produces by Roland Krause from Lion Biosciences Ag. Roland no longer works at Lion, so address all questions to Gert Vriend.


For support or WHAT IF related queries Email Gert Vriend at Vriend@CMBI.RU.NL

(C) G.V. April 14 2012