one kinase and its scaffold protein in a phosphorylated version is needed to be simulated. How to standardizes that and what water model shall i use?
I would like to do peptide map of a protein which is attached to PEG via lysines. Now the best approach would be to de-PEGylate it but then do the peptide map. But there is little literature on...
14 July 2024 5,634 2 View
I am having an issue regarding Phosphatidic acid topology generation for Gromacs 5.1.5 simulation. I would like to study the protein-ligand dynamics. Kindly help
03 June 2023 7,760 5 View
I have a phosphorylated protein ligand docked to my protein receptor, i would like to simulate the structure , but after adding forcefield using charmM , an error is occuring saying- "T2P not...
25 April 2023 451 6 View
The molecular simulation of two 50 amino acid long helical proteins forming heterodimer has ran 100ns then again ran for 50 ns. But the RMSD graph deformed. I have used gromacs 5.0 and saved it...
19 June 2019 6,966 7 View
I am working on fungal secondary secondary metabolites. Can I identify the biochemical natures of different metabolites present in the mixture with p-anisaldehyde -sulphuric acid and...
19 July 2017 949 3 View
How can I identify unknown metabolites in the crude fungal extract through LC-MS study?
22 August 2015 8,836 2 View
How to perform gromacs on a remote machine for proteins longer than 500 amino acids for atleats 120ns
01 January 1970 4,326 8 View
Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...
06 August 2024 1,989 3 View
Hello, I am currently analyzing some phosphoproteomics data, but I have peptides with multiple phosphorylation sites or phosphorylations together with carbamidomethylation or oxidation. How can I...
04 August 2024 8,432 3 View
Molecular docking software/ websites?
02 August 2024 8,704 7 View
Dear All, I am trying to transfect a pCDNA3.1 vector containing my gene of interest. The purpose is to figure out the localization of the protein of interest. I have fused the protein with GFP on...
31 July 2024 9,892 4 View
Hello , I established a stable cell line expressing GFP tagged to a centrosomal gene having G418 drug selection marker. I validated the stable line by IFA and Western blotting, results are fine....
29 July 2024 5,007 0 View
I want to do 2,3-butanediol dehydrogenase(BDH) enzyme purification to confirm its activity for 2,3-butanediol. Before that, I need to confirm which N or C terminal tagging is better for enzyme...
28 July 2024 366 3 View
I cannot confirm cell surface protein expression by flow cytometry even after transfection and antibiotic selection of cells. Does it take long for proteins to express on the cell surface? the...
28 July 2024 3,178 3 View
Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...
28 July 2024 2,136 4 View
I wanted to know whether we can observe the synergistic/antagonistic/additive properties of combinations or mixtures of compounds through docking analysis. But during docking preparation any...
28 July 2024 7,413 6 View
It has been long known that EDC carbodiimide and NHS easter's half life agains hydrolysis are highly related to pH. However, very surprisingly, not yet found a paper giving a table/chart of their...
25 July 2024 8,738 0 View