I have a protein PDB structure I’ve seen you this text，,I want to use Voronoia software to find the cavity of the protein and the amino acids of the cavity ,Can you help me to analyse it? I want to use the SURFNET software to find my cavity,can you help me to analyse? the following is my protein PDB structure.
My apologies for the confusion, but SURFNET was not written by our group. SURFNET was written by Laskowski. Perhaps you could reach out to that team, and they may be able to help:
SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions.
If you’re interested in using a similar software, you may want to try our 3V server:
If you experience difficulties using 3V, please do not hesitate to let us know.
ps — By the way, I just ran 3v on your pdb. Feel free to set whatever parameters you like, but I used 2 and 6 as probe radii. See attached results.