Debanjan Kundu

5 Questions 11 Answers 0 Followers

Questions related from Debanjan Kundu

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 2,391 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 3,246 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 9,292 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 5,986 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 5,668 3 View