Olatomide Fadare

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Questions related from Olatomide Fadare

Docking analysis of compds from gcms shows that FFA & waxes have high binding affinity 4 protein target - can this translate to in-vitro inhibition?

If docking shows that long chain hydrocarbons have high binding affinity for a particular target protein, can this really mean that the long chain HCs will have potent inhibition in-vitro or have...

01 July 2023 238 2 View

Why Compound is active in novelty induced behavior but not active during antidepressant study on mouse model experiments?

I have conducted a novelty induced behavior experiment, with mice as experimental animals, for a new compound and I observed significant activity (at very low doses) but when i carried out forced...

01 July 2023 2,200 0 View

Why does my tetrameric protein split up and move about as different units during Protein-Ligand simulation involving the protein and ligand ?

I have tried to do a 50ns of the GABA receptor (a tetrameric protein) with a ligand and after the simulation i noticed the different units of the GABA receptor moving about as i was playing the...

29 October 2021 3,665 1 View

Can a Big protein be cut into domains for protein-ligand interaction MD simulation?

If my protein is large and has many domains of which one domain has the active site that I want to study ligand interaction for with MD simulation, can I cut out the domain of interest in the...

03 April 2021 8,055 3 View

How to generate toplogy for a metalloprotein?

I want to do an MD simulation of a metalloprotein with an organic ligand using gromacs and when use gmx pdb2gmx for the metalloprotein stripped of the ligand i get the following error...

21 November 2020 2,737 1 View

Which version of gromacs can i use with g_MMPBSA program (5.1.x) to calculate Free Energy after Protein Ligand Simulation?

I am currently using gromacs 2020 for my MD simulation (Protein-Ligand) and i have g_MMPBSA 5.1.x installed. after entering the command, g_mmpbsa -f md_0_10_center.xtc -s md_0_10.tpr -n index.ndx...

06 May 2020 4,127 5 View

Why does Mac version of VMD crash when loading a 3000 frame .xtc file from gromacs md simulation?

I have VMD 1.9.4 installed on a MacBook Air that crashes whenever I am loading .xtc file from a 30 ns simulation on gromacs. The .xtc file opens on the VMD installed on a linux pc without any...

11 July 2019 4,998 3 View

Can a mutant protein be used as template for constructing a homology model?

I have the sequence of the protein that I want to model and I have two proteins with 3D structures that can be downloaded from PDB.org. The two likely template proteins being considered were...

30 June 2019 9,546 3 View

Can someone help with running autogrid4 on my windows PC?

I have installed the MGL tools, autodock 4.2 suite and pyMOL as well as discovery studios on my PC and i am following steps from the autodock tutorials. And when i get to Run autogrid and i click...

24 June 2015 6,507 7 View