16 Questions 23 Answers 0 Followers
Questions related from Saleha Hafeez
I have a single purified sample of trimer, dimer and monomer proteins purified through affinity chromatography. Is there a way to find concentrations of each protein in a sample? If total...
20 June 2023 2,716 7 View
We are inducing a periplasmic protein using 1mM IPTG at 37 degrees for 3 hours. We cannot centrifuge and remove supernatant the same day. So can we store the broth containing Bacterial cells and...
07 May 2023 7,712 4 View
In DNA gel electrophoresis my plasmid DNA is above DNA ladder which indicates nicked dna. Plasmid was purified by plasmid miniprep kit. My plasmid is not digesting. Enzymes are fine. Agarose...
08 November 2022 1,172 3 View
My protein is scfv 25kda which precipitates after puirification through ni nta chromatography. Protein precipitation is observed next day when protein is taken out from refrigerator. Is there a...
06 October 2022 3,146 4 View
Is there a way to break homodimer scfv and allow it to form a monomer scfv? Is there a way to convert homodimer scfv into monomer scfv consisting of 2 disulfide bonds at interface of dimer?
19 September 2022 3,205 2 View
Discovery studio is showing metal acceptor bond between ligand protein. What is the nature of metal acceptor bond? Bond is between iron of ligand and oxygen of protein Fe3O4 is the ligand
16 July 2022 3,258 0 View
Dear All, I docked a ligand using Autodock vina and performed MD simulations for about 100ns. I need help in analysis of the results. If we see the results can we say the ligand detached from...
01 April 2022 1,464 3 View
I have to simulate carbohydrate-protein complex on GROMACS. I have used GLYCAM webserver to generate a trisaccharide. Then I used acpype of Ambertools21 to prepare carbohydrate ligand using...
01 March 2022 5,940 6 View
I am new to MD simulations. Large movements in proteins occur at microsecond or more timesteps. My question is which one is timestep dt or nsteps?
24 December 2021 6,569 4 View
Can we use AmberS99 for antibody (protein) and Charmm36 for antigen (drug like small non-protein) in md simulations? Or do we have to use only one forcefield for both?
08 December 2021 2,030 3 View
I am using Ubuntu 20.04 LTS on Windows 10. Problem is Ubuntu is not detecting any of my GPUs. I was working on Gromacs and when I tried to run simulations on GPU it said GPU not detected. Gromacs...
28 October 2021 7,309 4 View
We used playmolecule to protonate the protein at pH 7.4. Gromacs adds hydrogen atoms. Is there a way in which we can prevent this addition and use the molecule as it is?
27 October 2021 6,762 4 View
We have to compare two proteins (wild type and mutant) Do we have to first perform protein stability test in water MD simulation and after that for function, protein-ligand simulations? Will...
22 October 2021 932 4 View
We are going from protein sequence to protein structure. Does MD simulation refine the protein structure? if we have to perform MD simulation then do we have to perform loop modelling and protein...
21 October 2021 1,303 4 View
I want to stain liposome with rhodamine. For this I need protocol.
21 April 2019 7,263 1 View
I am using probe ultrasonicator to disperse MNPs in ethanol for SEM.
26 January 2019 2,185 8 View
