Question: Homology Modeling With High Sequence Identity
0
gravatar for Raghul
7.0 years ago by
Raghul200
Italy
Raghul200 wrote:

Hi to all, When trying to build a homology modeling for a protein with high sequence identity (>80%)with PDB structure using SwissModel with "alignment mode" option, modeling was not done. Have anybody done something like this? Is it unnecessary to do homology modeling for same protein between very closely related species when there are very few changes between target & template? or on the contrary dont we miss something? I downloaded the original structure & used the "mutate" (SwissPDB Viewer)option to change 5 amino acids (which were the only differences between target & template). I did some model checking with procheck/whatcheck. After these the tool option in SPDBviewer highlighted these particular mutated amino acids have errors or impossible configurations! When mutating, an amino acid can adopt several possible confirmations & configurations, so which confirmation can i give to an amino acid when I mutate it? For eg Proline have very few! I am not a biochemist but I am just interested to see the effect of few changes at structural level in my protein?

thank you raghul

sequence homology • 2.2k views
ADD COMMENTlink modified 7.0 years ago by Vladimir Chupakhin520 • written 7.0 years ago by Raghul200
1
gravatar for João Rodrigues
7.0 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

I never used SwissModel, but I'd reckon you can even use a template with 99% identity. What was the error or problem you experienced? Why do you say the modelling was not done?

You can also try another server like PHYRE2 and see if you get along better with it.

ADD COMMENTlink written 7.0 years ago by João Rodrigues2.5k

thanks, I will check again

ADD REPLYlink written 7.0 years ago by Raghul200
1
gravatar for Vladimir Chupakhin
7.0 years ago by
Toledo, Spain
Vladimir Chupakhin520 wrote:

Modeller is the perfect choice. 80% is a high homology but I would recommend to use homology modeling and not a simple "mutate and optimize" strategy, because it will adopt correct conformation of the amino acid and optimize it's orientation (minimization).

ADD COMMENTlink written 7.0 years ago by Vladimir Chupakhin520
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