Pratyush Pani

7 Questions 5 Answers 0 Followers

Questions related from Pratyush Pani

How to generate topology for a phosphorylated protein?

I have a protein, for which I want to computationally study the effect of its phosphorylation. I was able to add a phosphoryl group to my desired THR residue and the structure looks fine. However,...

22 April 2024 8,560 2 View

Can FRET be done for two proteins outside the cell?

I have read several literatures regarding live cell FRET imaging and quantification over time. But is it possible to do it outside of cell, in vitro? I was recently told that it is possible but...

25 November 2023 5,542 2 View

Is there a software that performs D-NEMD?

Dynamic Non-equilibrium Molecular Dynamics

22 October 2023 7,686 1 View

Can anyone refer me to a simple protocol for Competitive Binding Assay using UV-Vis Absorbance method?

I have two molecules, both peptides: one being a receptor protein and other its viral binding substrate. Both of them have one wild type and 2 mutated variants. I have pretty much figured out how...

20 July 2023 6,954 2 View

Can anyone refer me to a good protocol for small peptide sequencing through GCMS?

I am currently trying to characterize a small peptide that was designed computationally and later synthesized and purchased from a manufacturer. I want to perform Gas Chromatography-Mass...

12 May 2023 1,647 3 View

How to process the protein and ligand Isothermal Titration Calorimetry (ITC)?

Hello, I am young researcher working in computational drug discovery and willing to perform experimental work, for which I am planning to start with ITC. Currently, I am reading relevant...

11 March 2023 3,394 3 View

System getting out of box upon simulation

I want to study the aggregation of a small molecule through classical MD simulation. For which I initially generated the topology of a single molecule using CGenFF and used them further in GOMACS....

01 January 1970 7,936 1 View