There is much software that is there for Docking but I was confused about how can I choose the right one from iGEMDOC,AutoDock 4 and AutoDock Vina.
I want to know the difference between these. please answer me regarding my confusion.
Thank You.
Nayan Prajapati
1. iGEMDOCK & Autodock Vina are widely used during the virtual screening process (where you have more number of compounds to dock to a protein). The process is simple and one after molecule is automatically screened.
2. Autodock vina requires few command line and manual operations, however, you can use GUI versions like pyrx, racoon, etc.
3. Autodock vina usually don't have results visualization directly, however you can use external software like pymol or discovery studio to analyse your results.
4. The efforts needed in iGEMDOCK is pretty lesser where you get results in a few clicks.
5. AutoDock is usually used in the case of grid-based docking where you wish to see to long performance rather just screening. A long run with multiple conformations will give you an idea on understanding the involvement of crucial amino acids and other bond formations.
6. As of today, AutoDock4 has 10974 citations, AutoDock vina has 13262 citations, and iGEMDOCK has 528 citations.
Considering these, you have to choose the tool based on your necessity and can't be one single conclusion. Even the forcefield parameters differ from one to another. However, on the whole, the molecular dockings itself have a huge set of known limitations like they predict molecules in static condition but the real system is not static. So, in the end, you need to perform molecular dynamics simulations to validate your dockings.
Freely Available: AutoDock Vina is Best if you want to dock protein-ligand. for Protein-Protein Docking you can use HDOCK server. (Less precise results)
Commercial: Glide (Schrodinger) for Protein-ligand, Protein-Protein, Protein-Peptide docking. (Very precise results)
AutoDock Vina is widely accepted for protein-small molecule docking and is slightly better in its prediction as compared to AutoDock. Also it is important to note that you will have to substantiate your data of docking through simulation and dynamics.
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