1. I prefer you see the resolution.. the resolution below 2A consider as good.

2. I prefer you to choose protein with a native ligand.. it will enable you to do a docking validation in your research method.

Dear @ Mohadese Mohammadi

You can choose proteins that are important for viruses, for example, viral proteins control and influence viral gene expressions in the viral genome, including viral structural gene transcription rates. Viral regulatory and accessory proteins also influence and adjust cellular functions of the host cell, such as the regulation of genes, and apoptosis. Also, it will be wiser if you choose protein with a native ligand.

If you search one protein in protein data bank.. there will be proteins in its apo form (do not bind to any molecules) .. and there'll be protein with molecules bind to it..

The molecules bind to the protein called native ligand.. native ligand can be drugs or any molecule

I prefer you to study the mechanism of the problem you are researching..

And then choose protein which protein have the most important effect, so if you inhibit the protein with your molecules, the mechanism will be stop..

If its about virus, you can choose main protease as inhibition of that can result viral death.

Adequate review of literature

dear scientist my opinion for you is to read some articles based on literature review you can chose your protein its nature and involvement in any pathways. my group is working on structural bioinformatics i warmly welcome to join us