Ahmed samier Mohamed

4 Questions 10 Answers 0 Followers

Questions related from Ahmed samier Mohamed

Is there any reference or tutorial for creating peptidomemetics in silico?

I would like to create peptidomemetics based on a certain known peptide in silico. For this I am asking if there can be any good references on this topic. (in silico specifically) What I Want to...

28 December 2022 683 1 View

MM-GBSA per residue energy decomposition positive value?

I ran a molecular dynamics simulation for a system that consists of a peptide-protein complex, the binding happens at certain residues. on calculating the MM-GBSA per residue energy decomposition...

08 March 2022 8,112 4 View

Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my...

01 February 2021 6,464 1 View

Best tool to build missing residues, minimize and validate a ligand model?

I am working on a ligand that is co-crystalized to parotein, but the ligand is missing some residues that makes it appear as if it was separated into two ligands! what I need is to connect them...

24 January 2021 4,167 7 View