I would like to dock an enzyme with its substrate. Can anyone suggest any free software which I can use and which has a tutorial provided?
For in-silico interaction studies u can use Patch Dock server (http://bioinfo3d.cs.tau.ac.il/PatchDock). Patch Dock results can be refined by submitting best 100 dockings to FibreDock server (http://bioinfo3d.cs.tau.ac.il/FibreDock/) or firedock (http://bioinfo3d.cs.tau.ac.il/FireDock/) . Interacting amino acid side chains can be visualized with VMD software.
myPresto, developed by colleagues in Japan, provides a useful software suite for that purpose
Anchal, Autodoc is so far the best software known to me and is freely available. All the best!
You can also use GOLD (Genetic optimization for ligand docking)software which is also freely available for docking studies,AutoDock is also a best software for docking studies..
I'm pubblishing a work in which I describe the interactions between a drug and an enzyme responsible for its biotransformation in a toxic agent. I used Vina, it's fast, accurate in finding the poses and free http://vina.scripps.edu/
If your substrate is a protein or a big peptide, Autodock is not going to help here....Autodock will accept a small molecule or a peptide which is having upto 32 rotatable bonds.
If your substrate is a protein you can go for HADDOCK online server
In my view ,you have few free docking available online such as Hex dock, auto dock, Mole grow and some on line tool you can fine ...
If u r substrate is not a protein, try autodock itself, its the easiest. Considering it as a ligand
Hey i guess patchdock is only for protein ligand... I want to dock a non protein molecule...into an enzyme
Olive, you can use ChemDraw suite to draw small molecule and convert into 3D, you can also try Marvinbeans, these two are freely downloadable.
There are some(for ex: http://www.click2drug.org/directory_PrepareSmallMolecules.html) online servers where you can draw and convert molecule into 3D.
AutoDock is good for docking even for the macromolecular docking also. I also recommend to use Hex as it is very easy to use.
autodock vina is better than going in for autodock 4 because of two orders of magnitude of processing speed and having a superior binding model predicting ability...and also its freely available!!!
Autodock package is the best free software that you can use moreover its easy to understand
Autodock is free and easy to use, you will get many tutorials in youtube. Also you can read my articles.
https://www.researchgate.net/publication/286246196_Molecular_docking_studies_on_InhA_MabA_and_PanK_enzymes_from_Mycobacterium_tuberculosis_of_ellagic_acid_derivatives_from_Ludwigia_adscendens_and_Trewia_nudiflora
https://www.researchgate.net/publication/236213990_Inhibition_of_VEGF_A_Novel_Mechanism_to_Control_Angiogenesis_by_Withania_somnifera%27s_Key_Metabolite_Withaferin_A
Article Molecular docking studies on InhA, MabA and PanK enzymes fro...
Article Inhibition of VEGF: A Novel Mechanism to Control Angiogenesi...
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