Hello all!
I am using Modeller to construct a homology model of my query sequence
(250AAs) from two template proteins (A: major protein of 225 AAs and B:
minor protein of 25 AAs). The overall identity of the query and template is
very high (~85%). There is a loop of 20-25 amino acid, which is constructed
using the template B.
To my surprise, in the final model, the constructed loop of about 20 amino
acid is very weird and is folding back into the protein (sandwiched between
secondary structure) resulting in numerous clashes. I feel this is unusual.
Could anyone suggest me the reason for this and the probable solution as
well?
Best,
*---*Thanks & Warm Regards*---*
Malkeet S. Bahia, PhD
Post Doctoral Fellow at the lab of Prof. Hanoch Senderowitz
PBC Indo-Israel Post-doc fellowship
Dept. of Chemistry, Building 211, Room no. 211
Bar Ilan University, Ramat Gan, 5290002, ISRAEL
Mobile: +91-9815988501 (India, WhatsApp only)
+972-584553434 (Israel number)