Zalikha Ibrahim

6 Questions 15 Answers 0 Followers

Questions related from Zalikha Ibrahim

Do all proteins have allosteric sites?

I want to search for non-competitive inhibitors for my protein of interest. There are so far no allosteric site published about this protein, but it has been reported that even after the...

14 October 2014 1,114 5 View

What if the ligand conformation of redocking procedure is not similar as seen in crystal structure?

I performed a molecular docking of a ligand-protein complex. The ligand has a missing fluorine atom, so I added the fluorine using pymol. The redocking procedure of both crystal and fluorine-added...

21 April 2014 6,918 12 View

Does anyone have experience performing mutation using COOT software?

I want to mutate an ALA to a CYS using COOT software, but I couldn't achieve my desired coordinates by clicking 'simple mutation' button. I found another button in COOT 'mutate and auto fit', but...

16 April 2014 3,385 3 View

Autodock: can anyone help with metal ions as co-factors in receptor?

I want to perform docking onto a calcium-dependent protein. Based on x-ray crystal structures, these calcium ions do not bind directly to ligands, but they do help in maintaining the structure of...

03 February 2014 4,990 4 View

Sampling rare conformation on protein using molecular dynamics simulation?

I want to see if there's any rare conformation on a protein. I have done the classical MD, but it seems too detailed that I couldn't see any distinct transition. Any idea on how to...

02 August 2013 3,792 14 View

Protein simulation with anisou atom record in the pdb file?

I want to simulate a protein using PDB file extracted from Protein Data Bank. After inspection, I noted that the protein atoms in the PDB has ANISOU atoms. In my understanding, this type of atoms...

09 July 2013 4,249 2 View