Nur Arshad

6 Questions 10 Answers 0 Followers

Questions related from Nur Arshad

RMSD plot from GROMACS output file .xtc did not start from 0ns. How to get the 0ns frame?

Dear GROMACS expert, I am currently having trouble to analyse the results from my simulations. After processing the output files using this command, gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o...

03 May 2024 7,057 7 View

How can I assess the rigidity and accessibility of docked protein-protein complexes in the molecular docking assessments?

Since one of the proteins contains Leucine-rich repeats (LRRs), this region may exhibit structural flexibility that could impact the binding interactions. Do I do molecular dynamic simulations on...

19 November 2023 8,054 0 View

Predicted structure for designed protein has poor qualityscore

Hi, I perform structure prediction for my designed vaccine construct using Robetta web server. And perform a validation score with PROCHECK to generate the Ramachandran plot and ERRAT scores. but...

01 January 1970 1,000 7 View

HADDOCK score is in positive value

I did two different protein-protein dockings for my bioinformatics project. First, I used the ClusPro blind docking method and then I tried the HADDOCK server where I needed to input a set of...

01 January 1970 5,520 3 View

Verifying restriction digestion on plasmids, two restriction sites used for digestion were close to each other

Hi, I am currently working on to digest a plasmid using two different restriction enzymes. And I found out that the two REs that I chose were very close to each other and I have had trouble to...

01 January 1970 3,623 1 View

Designing protein construct

Hi, I am trying to synthesise a custom DNA construct. My end of DNA construct has a 6x His-tag attached for purification later on. However, I am not sure if I should include the stop codon before...

01 January 1970 5,012 2 View