I have modeled a protein in MODELLER , the protein is about 200 aa residues,contains alpha helices and sheets , one helices turned into loop which has no role in active site, can further studies like docking be carried out.
The overall model quality seems fine in Ramachandran plot.
Thanks in advance !!
usally loop regions resulted from homology modelling tend to be missing regions from the template file, so before further proceeding to docking if you have a high quality model, you could run a disordered regions prediction using a specialized tool to make sure these loop regions are not disordered, then to perform a loop modelling approach to check that these fragments if really contain dynamic loops which should have more implications in folding thermodynamics if you further consider MD simulations.
you can use this tool for loop modelling
http://proteinformatics.charite.de/ngl-tools/sl2/start.php
and you can select from different tools of disordered regions prediction
https://www.expasy.org/proteomics/protein_structure
Most probably MODELLER did not find sufficient similarity for this region to infer the secondary structure.
The propensity of alpha helix or beta sheet of an amino acids is in seq decides the secondary structure of protein. But the loop region is highly hydrophobic in nature. Modeller did not find accurate template. That's why the region of secondary structures look like a loop. But in many cases structure is more conserved than sequence.
- Badges
- Science topic
- Similar topics
- Chemistry
- Biochemistry