Debanjan Kundu

6 Questions 15 Answers 0 Followers

Questions related from Debanjan Kundu

Is the stop codon to be added a part of the full length Gene sequence before the restriction site at the 3' end if I am getting the gene synthesised?

I need to get a gene synthesized commercially for expression in bacterial system. When I am providing the information for the gene sequence, do I need to include the stop codon before the RE site...

14 February 2023 8,921 0 View

How shall I prepare a protein PDB file in a particular pH for docking and simulation?

I wanted to prepare a protein at an alkaline pH for molecular docking as that is the pH I want to perform my in vitro assays in? I prepared my protein at the required pH through H++ server;...

14 December 2020 2,413 3 View

How Shall I perform Principle Component Analysis in GROMACS?

I have to perform PCA as a part of my results and analysis of protein-ligand complex docking using GROMACS 2018.8. How shall I perform PCA and interpret the results for the same? Any insights...

14 December 2020 3,270 2 View

Which of the five PDB files (DRGFIN.PDB, DRGMMX.PDB, DRGNOH.PDB, DRGPOH.PDB & DRGAPH.PDB) as an output from PRODRG Server do I need to use?

I have some protein-ligand complex to simulate on GROMACS version:unchecked. For preparation of my ligands, I submitted the extracted Ligand.pdb file and submitted it in the Prodrg server, Energy...

02 September 2020 9,319 5 View

Has anyone ever experienced that the FASTA sequence downloaded from RCSB PDB and the seqeunce in structure of PDB of the same protein not matching?

I downloaded a PDB structure of a protein and the FASTA sequence of the same protein. When I imported the structure in PyMol, the sequence represented in one subunit of a protein is only a portion...

02 July 2020 5,994 8 View

Whenever I am creating a PDB file from PDBQT file, it is automatically saving the file as Type: BIOVIA Discovery File Type. How can I undo this?

So, a few days ago I had installed the free software BIOVIA Discovery Studio Visualizer to analyse certain protein ligand interactions. I observed that the pdb files which were created in my...

15 June 2020 5,674 3 View