Hi Deepak Verma ,

Open source Autodock tools and its packages are best widely use docking tool. It has high accuracy as compared to other docking tools. Discovery studio you can use to generate publication quality images of interacting molecule. for autodock many online tutorials are available. its easy to use and time efficiant.

@Akshay Ware,

Thanks dear, actually I used AutoDock during my MSc. The same version is available from that time. After my masters I shifted in genomics field that why I asked to update my knowledge I also used MVD but never use DS. You people are regularly using so you can give better answers. Do you know other open source tools which gives publication quality pictures of docking

Hi Deepak Verma ,

You can use UCSF Chimera, or LigPlot+

@Akshay Ware Thanks dear, I will try LigPlot+ that seems new.

Ligplot+ will only give you 2D diagrams of all molecular interactions between the protein and ligand in a docked/PDB complex. It is not meant for docking.

To answer the original question, you should try and look up some benchmarking studies which compare the performance of various molecular docking programs w.r.t speed and accuracy. If you have access to both the software, best thing to do will be to do your own benchmarking study and try and see which of the two reproduces the binding pose of a ligand in any small crystal prt-ligand complex structure. Personally, I have never heard of Molegro virtual docker and Discovery Studio is well known and often cited. But most benchmarking studies would rank Glide (Schrodinger), MoE, GOLD and AutoDock as the best docking algorithms.

@Aditya Sharma

Thanks dear to adding more idea. Yes It would be more authentic if I will do my own comparison. I never use Glide and project cost will not allowed to purchase it. To test this software I have to search cracked version.

Thanks for you help.

Molegro Virtual Docker is one of the best docking programs.

If you have both, you can try to conduct a consensual study as the programs have scoring functions.

@Renato Costa oh great idea.I have Molegro. In present, I tried other tools suggested by other users. All are increasing my knowledge.

Deepak Verma

Do you know Dock6?

It is also an excellent molecular docking program.

Yes maintained by UCSF. I never use this. Is there any extra thing in this package?