Aziza Rahman

6 Questions 6 Answers 0 Followers

Questions related from Aziza Rahman

What are the criteria for Identifying Non-Covalent Interactions (π–π, cation–π, π–alkyl, etc.) in Protein–Ligand Complexes?

I am analyzing protein–ligand interactions and used Discovery Studio Visualizer (DSV) to identify various non-covalent interactions, such as π–π stacking, cation–π, and π–alkyl interactions. I...

05 April 2025 354 1 View

Why is HOH molecule coordinates missing in PDB files generated by CPPTRAJ?

I recently completed an MD simulation of a protein-ligand complex using Amber, and everything appeared to run without any errors. However, when I converted the trajectory file (.nc) into a .pdb...

27 August 2024 5,402 4 View

Is docking of metalloenzyme using vina futile?

I have seen many using AutoDock as an open source docking software for docking of ligand to metalloenzyme. Can Vina too be used for docking of a small molecule to a metalloenzyme? If not then why?

15 March 2022 1,329 3 View

How can I use the dlg file obtained from AutoDock in Amber?

After docking of a small ligand to a protein, I am interested in simulating the protein-ligand complex in amber. However, I donot know how to use the information in the dlg file. Any help in this...

25 November 2021 4,698 2 View

Is it necessary to check the protonation states of molecules before docking in a docking study?

I am trying to dock another ligand to a protein-ligand complex in autodock assuming the protein-ligand complex as the receptor. After adding hydrogens to the receptor, when I try to save it in the...

22 November 2021 7,699 5 View

How to perform MD based minimization of a protein before docking?

I want to perform docking of a protein with a small molecule caffeine. I had missing residues in my protein which I modelled through modeller. After going through many literature, I found that MD...

10 September 2021 7,595 4 View