19 Questions 16 Answers 0 Followers
Questions related from Thai Leong Lai
At a fixed voltage of 260V, electrophoresis of protein was faster in our previous batch of 1x SDS running buffer. However, the electrophoresis was much slower recently with much lower current...
08 December 2023 1,361 3 View
It was a large scale culture of a single strain. Only 1 of the flasks showed cell death while others just grew fine. What could cause contamination that contribute to cell death, given that the...
29 November 2023 2,003 1 View
What to do if ChimeraX software doesn't recognise the .chimerax file downloaded from SwissDock after docking? Besides, the zip file of prediction done was empty. Thank you.
19 March 2023 5,189 3 View
I am dealing with human epithelial cancer lines cultured in T-75 flasks. After trypsinisation, trypsin inactivation and centrifugation, the cell pellets collected were resuspended 30-40 times with...
04 March 2023 5,804 8 View
1) NH3 is generated from the substrate 2) NH3 + NADH + α-Ketoglutarate -> NAD+ + Glu In the reaction, samples with a higher substrate concentration should produce more ammonia and consume a...
18 October 2022 3,079 2 View
Does the stability change with stock concentration?
18 October 2022 4,574 1 View
Kinetics study was done.
18 October 2022 2,913 1 View
I wonder if this would work by default. Does the iron ion need special treatment before/during docking with other organic ligand? Can I treat the metalloprotein like other protein without metal ions?
21 August 2022 5,487 0 View
Should the water be included under ligand.pdb or enzyme.pdb? Could you please either the interactive or command line method to do so? Thank you.
15 August 2022 5,933 1 View
PDB formatted structures sorted by avg. pLDDT and complexes are sorted by pTMscore (unrelaxed and relaxed if use_amber is enabled).
11 August 2022 8,271 0 View
For the files from GitHub, I saw others use wget [GitHub link to the files].
11 August 2022 6,341 0 View
Does a better docking score or stronger binding energy between a mutant enzyme with its substrate always translate into an improved enzymatic activity? How should RMSD, RMSF, radius of gyration,...
08 May 2022 1,171 7 View
The volume per well is 90 μL.
08 May 2022 3,030 1 View
How to know whether the low enzymatic efficiency is due to low inherent activity of the homologue or other factors like the use of prokaryotic expression system, absence of fungal-specific protein...
08 May 2022 7,467 0 View
I read an article that the higher RMSF indicates the larger perturbation of protein structure and hence indicating a better allosteric modulator. I wonder if the RMSF value is expected to be high...
30 January 2022 3,450 0 View
Are structure-based peptide drug design and ligand-based peptide drug design mutually exclusive? If we have the crystal structure of the protease and design the peptide inhibitor based on the...
25 January 2022 4,625 7 View
If so, is there any way to separate the RMSD values of the peptide and protein from the RMSD values of the protein-peptide complex? The peptide is designed as the inhibitor of PPI.
20 January 2022 9,371 4 View
I am trying to dock my protein.pdb and ligand.pdb generated from different PDB files. Each of them have only one molecule (Mol A for protein.pdb and another Mol A for ligand.pdb). Is there any...
14 November 2021 412 5 View
According to WHO, "the categories of xenotransplantation procedures include the following: Solid organ xenotransplantation; cell and tissue xenotransplantation; extracorporeal perfusion...
04 July 2020 7,249 1 View
