I am having the full-length homotrimer coat protein's predicted model. I want to rebuild virion capsid (Icosahedral virion) by using this homotrimer. Capsid structure of this virion is available of chopped coat protein. I want to perform some study on the capsid made of full-length coat length coat protein. Is there any specific way to do that or any article available which talks about capsid rebuilding from single coat protein unit? I searched on google and it shown VIPER database which have a tool for PDB to VDB conversion by using BIOMT matrix. I don't know how to gat this matrix. I tried to use the matrix of chopped protein along with my predicted model to rebuild virion capsid.
Hi,
first you have to superimpose (eg, TM-align) the structure of your predicted CP onto the coordinates of the "choped" protein as found in ViperDB. Once this is done, then you can apply the 60 rotation matrices to build the full capsid. Keep in mind that, most likely, such predicted capsid will have many overlapping contacts between neighboring assymetric units, which are an artifact of this procedure.
Hi
Mr. Mauricio Carrillo-Tripp
I have done the alignment and got the backbone of both proteins in aligned format. But I don't After this alignment how to generate rotation matrix. I am having chopped protein in VDB format. I replaced one chopped trimmer with full-length predicted model and open in the molecular viewer. There it is showing the presence of full-length model in the entire capsid. But I am not satisfied with that result. Can you tell me how to generate rotation matrix for capsid structure determination. It will be very helpful for me.
Hi,
sure. You can find them here http://viperdb.scripps.edu/mat.php?tnum=60
They are the same for all icosahedral capsid in the viperdb convention.
- Badges
- Science method