Dewald Schoeman

4 Questions 5 Answers 0 Followers

Questions related from Dewald Schoeman

How should I rewrap and recentre my peptide-protein system?

Hi there, I’m running a 500ns MD simulation of 8 peptide-protein systems using GROMACS 2023 to investigate viral-host peptide-protein interaction. My protein (86 residues) is the same for all 8...

24 August 2023 2,049 0 View

How do I determine the position restraints for my protein-peptide simulation?

I have a protein-peptide complex that I would like to run an MD simulation on and I'm using the parameters that I got from a paper. The majority of parameters are quite clearly laid out in the...

07 June 2023 4,612 3 View

Web servers or software to simulate post-translationally modify protein residues?

I'm working with a viral protein that has been shown experimentally to interact with a host protein but the interaction is dependent on the viral protein being acetylated on 2 of its lysine...

26 September 2022 3,302 0 View

How do I identify/visualise hydrophobic interactions in PyMol?

I'm looking at viral-host protein-protein interactions and have used the HADDOCK web server to dock my host protein and viral protein. The paper I'm using as guidance for the interface residues...

31 March 2022 3,320 4 View