I'm not a protein scientist, but sometimes I need to look at a protein structure, for instance to check if a putative interaction motif is exposed on the surface and whatsoever. The problem is that I need to do this just 4-5 times in a year, therefore I never invested my time in perfectioning my script abilities on rasmol for example. It is really a pain to get back to the instruction manual every time. Now, I found this new online software which runs in the cloud without plugins: JOLECULE, maintained by Bosco Ho.
Jolecule is designed to make it easy to find and look at and identify residues and atoms. [...] Just edit the url, add "/pdb/' + PDB code. (For a new structure, the server fetches the PDB from the RCSB)For instance, here there is the glucocorticoid receptor bound to DNA.
With JOLECULE it is easy to save you preferred view, you can also annotating it and
share your protein annotation on the web with a simple link.
Pretty easy and very intuitive, you just need a PDB code and some patience the first time when you address the server to a new PDB (the server is still a small one). The good news is that once loaded, the PDB is cached on Jolecule server forever.
If you are just curious to simulate the binding of any molecule (written in SMILE) on any PDB, and you don't know nothing about docking (like me) just play with SWISSDOCK (and than, speak with someone on the field).