Last time I gave a presentation about different papers describing Molecular Dynamics simulations of TCRpMHC (http://blopig.com/blog/?p=648&preview=true). This time I extended this to more of my own work. The focus of this talk was about the motivation why to choose a certain system and which requirements if must fulfíl for reliable conclusions. In short they are:

1) A larger number (>100) of experimental values (e.g. some kind of binding, immunogenicity, etc) of a certain TCRpMHC system. These values should be provided by:
– the same group
– the same HLA/MHC batches
– the same binding conditions
– in the ideal case in the same manuscript

The values should NOT be from a database since different experimental groups come to extremely different results for the same complexes as several examples show e.g.:
The binding IC50 affinity values of PKYVKQNTLKLAT to DRB1*01:01 range from 1nM and 600nM (IEDB entries).

2) Structural data exactly matching the systematic experimental data mentioned above. If multiple structures are involved they should be published by:

– the same group (in the ideal case even published together with the above mentioned data by the same group)
– be contemporary

Data which fulfil the above mentioned criteria is quite hard to find since most biologists are mainly interested in some fancy, however, rather anecdotal examples and rarely in systematic data production.

Once one has found such a system a large number of Molecular Dynamics simulations can be performed which will yield systematic differences not just differences originating from random events or data bias.