i would like to learn drug design specially docking but i dont know how to start since i have no previous experience in this field as being a polymer chemist
Although there are several softwares for docking, most of them are paid. Autodock is free and can be used at the user's disposal. Apart from that, SwissDock is also a growing docking web server.
The basics of docking lie in identification of the active site in the receptor protein, fitting pose into the pocket, exploration of the chemical bonds or other interaction between the ligand (docked molecule) and the receptor protein and energy estimation of those interactions.
Great you are interested. Kindly first decide in drug design your goal and then star molecular modeling. Various tutorial at you tube and also read discussion at research gate it help in problem solving. Still problem you put at research gate
I too am new to molecular docking but have found the following videos very useful:
https://youtu.be/EI7ojGoLLUk - basic 5 min intro to docking
https://youtu.be/k6tqCeDIwEk - full introduction to docking with Autodock
https://youtu.be/pt4F6hnDvBk - general interest, shows a couple of applications of docking
https://youtu.be/l-_6tbk_ey0 - intercalation of proflavine into DNA
My interest is in using the docking software to screen potential anticancer drugs via their ability to intercalate into DNA. Research in this area is much more limited compared to the use of docking for ligands interacting with proteins. A very recent paper (Evaluation of Docking Machine Learning and Molecular Dynamics Methodologies for DNA-Ligand Systems - PubMed (nih.gov)) uses Molecular Architecture which is a docking workflow that allows screening with different algorithms. Its best results in terms of ligand conformation were with Consensus although this is actually a combination of AutoDock and Dock 6.
An important consideration is the use of molecular dynamics simulations for further refinement after docking. AutoDock assumes a rigid protein/DNA binding site and a flexible ligand. However, the DNA flexes when it interacts with a ligand in order to accommodate it so really this needs to be factored in and molecular dynamic simulations via GROMACS NAMD does this. I hope this helps?