Mostafa Zeinal

7 Questions 8 Answers 0 Followers

Questions related from Mostafa Zeinal

What basis set should be used to optimize the small molecule for further MD simulations?

I have created a handful of small molecule candidates and I want to perform MD simulation what basis set should I use to optimize their structures? if it's possible could you provide the DOI of...

28 November 2022 1,181 5 View

How plot the correlation of impact of one element to the result using python?

I am working on a small data frame, (result, element1, element2), and I want to correlate the impact of these elements on the result using python. These elements are amino acids residue and result...

19 November 2022 6,587 4 View

How to convert this protected c-glycopeptide to the desired molecule? is it even possible?

Based on this article https://doi.org/10.1021/acs.orglett.2c01501?urlappend=%3Fref%3DPDF&jav=VoR&rel=cite-as I wanted to synthesize the desired molecule from the final product of the...

14 November 2022 9,498 2 View

How the remove protection groups from this molecule to yield c-glycoamino acid?

As the title of the the article claims, the final product should be a c-glycoamino acid but I can not understand and find the reactions for removing the protecting groups. I would be happy if some...

02 August 2022 5,319 0 View

How can I find the different methods of glycosylation of amino acids (Trp, Phe and Tyr to be precise)?

I'm looking for different ways of fusing a sugar molecule to an amino acid. I'm having difficulties finding the proper literatures to study them, and I was wondering if I could find some help here.

03 July 2022 5,003 2 View

Which forcefield goes the best with Gromacs, to obtain the binding affinity and carry out further analysis of binding of a ligand to a protein?

I wanted to start the molecular dynamics simulation of a couple of ligands. Selecting a forcefield has been a difficult to do, for me. I was hoping to the ResearchGate community could help me.

10 May 2022 2,751 1 View

Is it possible to run autodock-gpu on google colab, if yes how so?

I want to dock a handful of ligands to a receptor. I found out that the new fork of autodock, autodock-gpu, has been developed for accelerating docking process by using gpu instead of cpu. I was...

26 April 2022 3,510 3 View