Mochammad Arfin Fardiansyah Nasution

5 Questions 11 Answers 0 Followers

Questions related from Mochammad Arfin Fardiansyah Nasution

What is the tolerable RMSD value when we validate the docking simulation parameters from the standard's pose?

To validate one of our research methods, we used the PDB ID: 5MRK (Structural basis of Zika virus methyltransferase inhibition by sinefungin) as our standard. When we do the docking simulation of...

02 October 2017 6,692 6 View

Is there any way to predict oral bioavailability for natural product compounds using computational method?

I believe that we cannot consider Lipinski's RO5 since it does not apply to natural product compounds. Hence, I am not sure either Veber/Egan/Ghose rules can be implemented as well

16 May 2017 4,260 4 View

Can we do molecular docking and molecular dynamics simulation in a different types of force field ?

In our latest experiments, we did a molecular docking simulation by using "CHARMm" forcefield and it went well. However when we were doing molecular dynamics simulation by using an exact same...

15 June 2016 7,046 3 View

Is the $1000 VGA card worth to buy for MD and docking simulation ?

Our colleague suggests that, by bought the $1000 VGA card to our computer, our simulation would run incredibly faster, and can easily achieve 100 ns MD simulation in less than a week even though...

02 April 2016 4,965 8 View

Can I use Thermodynamic Integration MD Simulation approach by using GROMACS?

So far we're using MD simulation to get RMSD result of the protein-ligand complex and see which one is the best. So far we didn't have the tutorial for doing Thermodynamic Integration MD...

24 May 2015 2,242 3 View