Supriya Hakeem

8 Questions 13 Answers 0 Followers

Questions related from Supriya Hakeem

How to define the binding site comprising selected amino acids in iGemdock?

I have a protein and want to carry out the docking in iGemdock defining the amino acids as binding pocket. How to prepare the binding site and load it in "loaded file" in prepare binding site wizard?

01 December 2017 6,368 3 View

Can anyone suggest reliable free docking software/server for protein ligand docking other than Autodock Vina?

I intend to check the autodock vina results by cross docking , which is the best tool to use for this purpose??

06 November 2017 9,131 6 View

Is extensive molecular dynamics simulation say 200ns feasible for homology model?

i have modeled a protein and to check its stability and dynamics i carried out md simulations for 200ns, however the rmsd plot shows stability around 100ns (rmsd around 4) and it continues till...

01 November 2017 9,585 6 View

Can docking and virtual screening be carried out on refined Homology Model?

I have build the homology model of the protein , which had passed the validation tests like procheck and prosa.I have carried out the 20 ns molecular dynamics , however there are certain changes...

18 May 2017 9,292 6 View

Can catalytic domain of a particular protein be modeled and virtual screening be carried out??

I have a protein of around 600 residues , when the protein was pdb blasted no suitable template was found for homology modeling.However when its catalytic domain of around 200 aa was taken alone...

09 May 2017 9,735 7 View

Is it followed that while homology modeling some expected scondary structures turn into loops?

I have modeled a protein in MODELLER , the protein is about 200 aa residues,contains alpha helices and sheets , one helices turned into loop which has no role in active site, can further studies...

03 May 2017 601 4 View

What do hydrogen bonds formed post docking other than the active site imply??

My query could be trival.I have docked an ihhibitor-protein complex and defined the active site of the protein. Ligand was placed roughly at the active site for the docking .After analyzing the...

18 March 2017 3,091 8 View

Why are there broken bonds in ligand pdbqt out file in PyRx Auto Dock Vina?

I have carried out docking in PyRx Auto Dock Vina ,However there are broken bonds in ligand pdbqt file when visualized in Pymol. I have tried changing the exhaustiveness parameter and changing the...

15 March 2017 7,040 2 View