[modeller_usage] What structure is better ??

[cristian obiol <>]

Dear Modeller users,
I have constructed a homology model of my human protein starting with a 
template of the yeast variant. The first problem I faced is that both 
proteins are very different, with only 23%  homology.
To solve possible errors in the best modeller structure I also carried out a 
6ns molecular dynamics asuming that minor changes would happen.
But I'm not sure if the first structure is the best one. And the option to 
performing a molecular dynamics for each modeller structure is very time 
consuming, moreover the RMS backbone deviation for the first five or ten ones 
is very small (0.8 to 1.1 A).
Here it's my question : What is the normal protocol in order to obtain a good 
enough final structure ? Can I assume that choosing the following structures 
and performing a molecular dynamics simulation I will get almost the same 
final stuctures ?

Thanks in advance for any suggestion.

Cristian Obiol
Biological Systems Modelling
and Drug Design Research Group
University of Barcelona