Shamali Abeywardhana

5 Questions 9 Answers 0 Followers

Questions related from Shamali Abeywardhana

How hydrophobic interactions effect on binding affinity in protein-ligand docking?

Dear All, I'm doing protein-ligand docking using AutoDock Vina and analyzed interaction between protein and ligand using Protein-Ligand Interaction Profiler (PLIP). i want to know is there any...

01 March 2023 1,006 1 View

Are there any molecular dynamics simulation web servers which is more robust and accurate ?

I need to run molecular dynamic simulation for a protein-protein complex which i obtain from HADDOCK server. Are there any web servers which i can run md simulation? If yes ,could anyone suggest...

26 February 2022 9,464 4 View

Shall I need to do a energy minimization to any protein structure which was refined using 3Drefine or Galaxyrefine servers before model them?

Sometime this may be a silly question because I'm new to this field. In 3Drefine server, it mentioned that it applies atomic-level energy minimization on the optimized model using a composite...

01 February 2022 8,143 4 View

Is Energy Minimization before and after protein-protein docking essential for a best result?

Actually I'm new to this field. I did structure validation by PROCHECK and ProsA servers for my protein structures after modelled them. Do I need to proceed energy minimization before...

31 January 2022 9,038 2 View

Can i use pymol mutagenesis tool to edit mutations in a PDB structure?

I made pdb structure from SWISS MODEL using reference sequence which i obtain from the NCBI. So now i need to mutate the structures of that protein. I'm going to edit this mutations using pymol...

23 November 2021 1,883 4 View