I am working with modeller and I would like to know the order of loop refinement (for example starting with loop3, then loop1 and then loop2) has any effects on the final model?
Hi,
there is no definite answer to your question. Assuming all loops to be distant from each other, order likely does not matter. However, loops interfere with each other due to their influence on back bone stability - which sounds trivial, yet is actually a bit too brief to be 100% correct.
With modeller, why not model your loops simultaneously? See http://salilab.org/modeller/manual/node34.html
This would fix adjacent residues (if not mistaken).
Or did I make a wrong assumption?
One more thing: My personal experience is that modellers loop refinement should in most cases be refined further with an appropriate MD approach.
In case this does not answer your question, you should be a bit more specific on your structure and your approach, because my description was a bit superficial - as was your question ;-)
And, of course, you can always ask the developers: http://salilab.org/modeller/discussion_forum.html
In my experience they are indeed really helpful.
HTH,
Christian
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics