Docking And Molecular Dynamic Simulation ??

Question

[Dollas Salleh]

Hi,

I'm new in Computational Biology area. Currently I'm working out on predicting the 3D structure of my target protein. For the info, I have already built the 3D structure and undergoes some refinement analysis. Now, I am looking forward to run docking and molecular dynamic simulation for my 3D structure of the target protein. But I don't have any idea how to start the docking and MD simulation. I have already tried to study some literature. But, I'm noticed I seem lost. I would appreciate if any of you can guide me for the above matter.

thanks a lot.

[Vladimir Chupakhin]

read the articles with examples on homology modeling, docking and MD simulation - there are a bunch of them starting from 1998-2004.

Answer 1

[vijay]

Hi Rashid,

Do let us know if it is protein-protein docking or protein-ligand docking?. In both cases, you need to narrow down to what kind of study you are going to perform. Same is the case with simulation too. You need to understand the biology behind your docking and simulations. There are excellent tools that can get these job done for you. However, these processes should be justified biologically.

[Dollas Salleh]

Actually I would like to perform protein-ligand docking. But I have no idea how to get a required ligand. The protein structure that I used was alpha beta hydrolase enzyme. I already identified some active site like catalytic triad residue. But how about ligand. How can I get ligand that suitable with my target enzyme for docking purpose?? Thanks..

Answer 2

[Dollas Salleh]

Ok. Now im understand after some literature reading. Thanks a lot for give some advice.

Answer 3

[biodano.geo]

Hi,

you can use Bevan Lab tutorial for MD simulation ligand-receptor complex.

if you've problems first see Bevan lab Lyzosime in water. if you haven't expertise in unix command, you can go for my tutorial of unix. Link: https://github.com/georopon