I followed the steps mentioned by John W. "(To find a native like structure I created 100 models for 5 different template combinations with and without loop modelling and with and without MD refinement, and I found that no loop modelling and no MD refinement gave me the best models.
I took my 5-10 best models as ranked by dope and the objective function followed by PROsa analysis. Then I further analyzed the 5 or so best via procheck. IMO brute force and sheer numbers are the best way to determine emperically what combinations of settings will work best for you.
I would definitely try no loop model and no MD and always do 100 models minimum.
Cheers.") - John W.,
After choosing the best models, based on the gap (where no template structure was available), i performed slow loop optimisation.
As I am new to modelling, I don't know how can I optimise my model more accurately
http://sites.google.com/site/piyushdiyora/
The above link has an image before and after optimisation.
Should i optimize other parts of he model, because there are several high peaks.
Second question is,
I am working on Dos1 protein from Fission Yeast. Sequence blast in Protein data bank provided 75 results. Out of these none of them were completely identical, but only part (fragment around 80 - 120 amino acid long) of the Dos1 sequence was identical to the (fragment) reference templates. Similarly other part was identical to other reference template. Based on such analysis, I went through all 75 protein 1) extracted the part of the sequence from reference template and then aligned with the Dos1 protein (http://sites.google.com/site/piyushdiyora/home/second-page).
My question is 1) As these fragments are from different protein having different 3d structure, HOW RELIABLE WILL BE MY PROTEIN 3D STRUCTURE?
2) If I want to build a model based on the reference template (created by joining all the fragments), how should i do it? I dont know how to manually modify the sequence file (which will be used by modeller)
Thank you in advance :)