IHM Meeting Summary Sep 21 2017

IHM Meeting Summary Sep 21, 2017

Attended by Ben Webb, Tom Goddard and Brinda Vallat

1. Representing predicted contacts in the dictionary (issue 41):

   This issue has been raised by a user. One of the methods used to predict residue-residue contacts is evolutionary coupling from deep sequencing methods. These predicted contacts are then converted to distance restraints used in modeling. Although these are being addressed in the modeling dictionary extension, we may need to include definitions in the I/H methods dictionary to account for the multi-scale nature of I/H models.

   There are two approaches to address this issue:

   • Create a generic category to represent distance restraints that may be obtained from different methods and define method-specific details in separate categories. The advantage of this approach is that we can avoid repitition of terms involved in defining distance restraints in different categories. This approach is feasible only if we can decouple method-specific details from the definition of distance restraints.

   • Create separate categories for distance restraints derived from different methods and include method-specific details within each category. The crosslinking categories in the dictionary currently follow this approach and were created based on IMP examples available at the time. This approach is preferable if method-specific details cannot be decoupled from the interpretation of the distance restraints. In case of crosslinks, it was not possible to decouple the ambiguities in crosslinks from the definitions of the distance restraints.

   We need actual examples of distance restraints obtained from different methods to figure out which approach can be adopted.

2. We also discussed the scope and contents of the grant proposals being submitted in the near future.