Changing the conformation of bound protein chain to its unbound state
0
0
Entering edit mode
5.1 years ago

If I want to carry out an unbound docking of the 2 chains of a hetero-dimeric protein but the individual unbound structures are not available, how do I change the structure of the bound partners to remove any native-complex structure bias that the 2 chains might have ?

I am using ZDock, a rigid-body docking algorithm. I thought of randomizing the side-chains of the surface residues of the 2 chains using GROMACS. I thought of running a simulation at a higher temperature for a short time span. This may randomize the surface side chains. The only problem is I have a large number of complexes which do not have unbound structures and such simulations take days to finish.

Are there any other methods of obtaining unbound structures from bound ones which are not time-consuming?

protein-protein docking • 1.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 2500 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6