i'm having some problems with 2 proteins that have 140 and 150 residues respectively.
By now i have generated only 1000 models (i intend to create 10000 in total), but i'm not having clusters at all :/
I read somewhere that the abinitio method (related to modelling) works on protein with less that 100 residues. Is that correct?
What can i do to overcome this problem?
I was thinking that (since i don't have any structure as a reference for my protein) on the total of 10000 models i'll select the structure with the lowest energy and i'll use it to perform a replica exchange molecular dynamic simulation, in order to be able to search in a more proper way the potencial energy surface of the respective protein.
What do you think about it?
Do you have any suggestion? maybe a different method/software?
Best regards to all of you :),
Carlos Navarro Retamal
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problem with modelling of protein (140 and 150 residues respectively)