i have done protein- ligand docking and then simulation of this dock stucture after that i want to analyse my results
Hi,
file:///C:/Users/Acer/Downloads/paper.pdf
https://www.researchgate.net/publication/268515808_Molecular_dynamics_simulation_of_propofol_bound_to_human_serum_albumin_using_linear_interaction_energy_method
http://pubs.acs.org/doi/abs/10.1021/ja00387a046
These are some the papers. Hope this helps you.
Regards
Conference Paper Molecular dynamics simulation of propofol bound to human ser...
thank you Eduardo and Danish
please send me the link, which is freely available for download
Hi Vinod,
You need to have a couple of things in mind before you do this:
1) Did you minimize your structure prior to simulating it? What was the energetic signature of your system?
2) Length of your simulation should be significant for the results to matter.
3) Are your results reproducible? Run the simulation again using a different seed number, for any analysis to matter, you need to have results that are reproducible.
Apart from this - what do you mean by analysis? There are a number of things you can look at e.g.
1) The energetics of your ligand and its 5A radius i.e. binding site residues?
2) Hydrogen Bond Network
3) You could do thermodynamic integration. Conventional Implicit solvent approaches of GBSA and PBSA.
These are some from the top of my head - and there is extensive literature out there on these and many other methods. You should frame your question in perhaps a less vague way to get a response that maybe more productive for you.
Good Luck.
Best,
/A
I agree with Ashar. Along with literature search you can consider all the above points suggested by Ashar during analysis.
I am looking for graphical analysis ant its interpretation, which is I found after simulation
Hi
Interaction analysis and energetic analysis are basic analysis you have to do these. Next based on your problem you search for your answer in MD trajectory like for any:
Conformation movement, visualize your trajectory
Secondary structure changes, go for secondary structure analysis.
Here are the links which can be useful in your study:
http://www.sciencedirect.com/science/article/pii/S1093326310000264#
http://link.springer.com/article/10.1186%2F1471-2105-14-S14-S6
Docking analysis through Autodock, Glide-SP and Glide-XP can be found in following paper
DOI: 10.1007/s10867-013-9299-7
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