Zalikha Ibrahim

5 Questions 13 Answers 0 Followers

Questions related from Zalikha Ibrahim

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 6,854 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 3,338 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 4,948 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 3,739 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 4,200 2 View