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Questions related from Joydeep Roy
I aim to perform a direct co-culture experiment between cancer cells and macrophages. My targets would be to study the altered metabolic pathways in cancer cells mediated by macrophages. I wanted...
05 June 2025 9,634 3 View
Currently, I work with a kinase which itself also gets phosphorylated. It needs to get phosphorylated for activation. Probing with the phospho-kinase antibody for a specific residue like Threonine...
24 October 2023 3,524 2 View
Currently, the localization study for my target protein because of another protein B has to be performed using confocal. It had been confirmed using Western Blot. 1. I wanted to know if it is...
06 October 2023 8,238 3 View
After performing some siRNA knockdown studies and overexpression studies I wanted to check my target protein localizing to the nucleus. After that I wanted to know the effect of localization on...
03 June 2023 1,163 0 View
Currently, I wanted to perform an experiment where I have to perform a drug treatment and siRNA transfection together. What shall be the way to design the protocol? Shall I perform the drug...
13 February 2023 6,863 2 View
Currently I work on endometrial cancer and I work on the gene PAK1. I had prepared knockout in endometrial cancer cells like Ishikawa but when it come to making knockout cells in AN3CA I have a...
29 November 2022 6,229 3 View
I work on a particular kinase whose partial model is only known through PDB. Ideally there is a site called as "Alpha fold colab" with the help of which I could generate the model. But within the...
04 November 2022 2,340 3 View
Currently I was trying to computationally predict the structure of a protein which acts as a kinase inhibitor using the tool I-TASSER. But had a confusion with the selection of the results. Top 5...
19 May 2021 1,222 0 View
I work with siRNA transfection in endometrial cancer cells where 72 hours after siRNA transfection, the cells reach a maximum of 65% to 70% confluency. In contrast, 95% to 100% confluency is...
01 January 1970 4,065 1 View
I wanted to perform a molecular dynamics simulation for a kinase and wanted to know how to generate mdp files for adding ions after solvation ? I could successfully generate the topol.top files...
01 January 1970 2,201 4 View
I need to clone a gene (2KB sequence) from one plasmid to some other plasmid which needs to have a fluorescence tag. After proper sequencing, I could find there is presence of the stop sequence...
01 January 1970 7,958 3 View
I work on a particular kinase molecule and would like to know whether it is possible to phosphorylate it at tyrosine residues using Pymol tool. I know for some residues like Ser/Thr it is...
01 January 1970 8,911 2 View
I want to perform an MD simulation for the phosphorylated protein. But whenever I add phospho-group to the structure using Pymol tool, the MD simulation is not executed at all because it...
01 January 1970 6,466 5 View
I get a fail result for Verify3D option in SAVES almost every time for the structures designed. I would like to know is Molprobity score sufficient in terms of reliability for the purpose of...
01 January 1970 7,648 3 View
