Gert Vriend
EMBL Meyerhofstrasse 1, 6g117, Heidelberg, Germany

The program WHAT IF provides a multitude of tools that can aid with modeling, drug design, structure description and comparison, mutant prediction, inverted threading, etc. One of the many tools is automatic model building by homology from a given alignment with the sequence of a known structure. The three models submitted for the model building by homology competition were generated using this fully automatic method (only a few manual interventions were made, and those are listed in the submitted file headers).

Given a perfect alignment, this method normally leads to very good models, although many problems still have to be solved. We routinely use a set of 25 pairs of structures that can be modeled back and forth. This dataset has been selected to fulfill the following criteria:

During the demonstrations several typical problem cases can be discussed. The quality of the model will never be better than the quality of the structure t was based on. Therefore the program WHAT IF provides extensive structure verification tools. These can be used to check the starting structures, but also to verify the final models. In several of the submitted models WHAT IF detected errors in the final model. I think (we will see it at the meeting...) that these are the result of poor sequence alignment. This is a different problem from the one I concentrated on, but it is nice to see that programs can detect these problems automagically. At the meeting we will see if these error detection techniques actually work or not. In any event, they can be discussed during the demonstrations.

P.S. WHAT IF is not a commercial product. It is distributed under restricted share-ware conditions.

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Last modified on 1-11-95