Senal Dinuka

9 Questions 10 Answers 0 Followers

Questions related from Senal Dinuka

What is more abundant in human cells? Beta or alpha glucosidase?

I am working on the well studied glucosidase - cancer relationship. During the work I have come across that beta-glucosidase is less abundant in cancer cells nevertheless human cytoplasm where...

10 October 2019 3,882 2 View

How to plot a reaction profile?

I have obtained zpe corrected energies for reactant, TS and product states. I can plot a general scattered plot using MS Excel (but not that great). I would like to know how to plot a reaction...

06 June 2018 9,169 3 View

Suggestions for charge calculation (delocalized)?

I have modeled an oxocarbenium ion like transition state (at B3LYP/6-31+G* level of theory) with overall charge of -1. I would like to calculate and check partial charges for the molecule. So far...

06 June 2018 540 3 View

Molecular docking/MD simulation to analyze TS stabilization?

I was able to successfully locate and confirm TS for my glycoside hydrolysis reaction. As the next step i thought performing molecular docking followed by SMD QM/MM calculation. In doing so i...

05 May 2018 2,936 5 View

How can I use spartan out files instead of gout in Amber 16?

I have been using Amber16 MD suite. As far as I have come a across respgen program in the suite only supports Gaussian output file as the preliminary input. Due to the fact that I follow Spartan...

10 October 2017 4,228 1 View

What is multiple ligand docking approach?

Can someone please elaborate me on the idea of multiple ligand docking approach and how it is done? What really can be predicted using this approch? Thank you.

02 February 2017 1,410 1 View

Simulated annealing in PyRx time consuming?

I have used LGA and found the results very much promising. Currently i am into simulated annealing with only 100 small molecules and found it has not moved forward even after running for a day. Is...

09 September 2016 4,428 2 View

How to perform QM Reaction study on Enzyme Inhibition?

For MD Simulated protein-ligand complex I have extracted the ligand and the reacting residues(as mentioned in literature) for further kinetic study. I have imported this model to spartan software...

01 January 1970 9,112 7 View

What is the best way to analyze binding energy for a small molecule docked in to several snapshots?

I have run vina for 6 snapshots of pre equilibrated cystal structures with several ligands. Now I have 6 vina energies per small molecule. What is the best way to analyze and filter results? I...

01 January 1970 3,508 4 View