Pousali Mitra

8 Questions 10 Answers 0 Followers

Questions related from Pousali Mitra

Cyclization should be performed before mutation or after mutation of a linear peptide sequence by in-silico method?

I have a doubt on in-silico modeling. I want to cyclize a linear peptide sequence by in silico. Which is more favorable method I don't understand. There is 2 pathways- 1. I can cyclize a linear...

13 June 2024 2,406 2 View

How can I calculate average dG MM/GBSA energy from selected frames of MD trajectories?

I need to calculate dG MM/GBSA energy through the MD simulation trajectories. From RMSD values I selected last 400 frames from MD trajectories. I ran thermal_mmgbsa.py script, but it calculates dG...

23 May 2024 9,944 5 View

How to find out per residue contribution to total dG binding energy of a protein-peptide complex?

Hi, I did dG MM/GBSA calculation for a protein-peptide complex. I want to know the numerical value of contribution of each residue of peptide to that total dG binding energy. How can I do that?

29 January 2024 7,877 4 View

How to run a job for dG calculation of protein-protein complex that takes less time?

I want to calculate dG binding energy of a protein-protein complex binding site. I choose the antibody as a receptor and the antigen as a ligand. Also I selected 10A distance from ligand for...

07 January 2024 7,146 0 View

Which scoring is more accurate to identify the best conformation of a particular ligand, epik state penalty or MM/GBSA calculation (dG)?

I have a doubt about choosing best conformer of a particular ligand. This ligand has 6 different tautomer and isomers, now one enantiomer has higher state penalty compare to others, but when I...

03 July 2023 6,315 0 View

All crystalized water molecules are necessary in binding site when you prepare your protein?

I have prepared a protein in 2 ways, one in which I kept only constraint co-crystalized water molecules i.e. crystalized ligand bind with those water molecules and deleted all other water...

06 March 2023 8,751 2 View

Which factors should be the main reasons to explain ligand stability in binding pocket except counting interactions?

I have docked some ligands with target (protein). I observed that, ligands which have more hydrogen bonds and hydrophobic interactions with protein give poor binding energy (less negative)....

01 March 2023 6,761 2 View

What is the reason that in Maestro, job is died automatically?

I am started to working with Schrodinger software. In Maestro no application is working here. When I applied ligprep tool under Maestro the job is automatically died. I can't understand how to...

23 October 2022 2,432 5 View