I would like to ask you how can I select a set of MOE descriptors. I have built a model based on 16 2D MOE descriptors and I want to calculate them for a new set of compounds in order to predict their activity using the workflow I am trying to implement in KNIME. Can you help me?
Thanks a lot in advance,
If you have built the model with MOE nodes you can use the "Model Evaluate" node to calculate the model predictions. the Model Evaluate node will automatically calculate missing MOE descriptors.
If you have built the model with a non-MOE node you need to precalculate the descriptors.
You can get enter the descriptor codes directly in the "expert" tab of the "MOE Descriptor" node or select the descriptor families the descriptors belong to in the 2D tab.
The only thing to remmeber is that if you use partial charge based descriptors (Q_) you need to make sure to use the same method for calculating partial charges as has been used for training.
If you need further help, please contact me at firstname.lastname@example.org.
EDIT - Just saw Guido beat me to a response by 1min, so probably ignore my reply!
I may not fully understand the question (apologies if this is the case), but if you want to calculate 2D MOE properties within KNIME using the MOE nodes, then in the latest release of the nodes this is accomplished with the "MOE Descriptors" node (formerly "QSAR Descriptors"). Depending on exactly which 2D descriptors you used building your model, you may have to select a number of the checkboxes in the MOE Descriptors 2D panel. You can then use a Column Filter node to remove all but the descriptors of interest (if you want). Does this help? If not, I'm sure Guido will be able to help further!