Protein-ligand docking is a computational method used to predict how a small molecule (ligand) binds to a target protein. There are many web servers and tools available for this purpose, catering to different needs such as ease of use, accuracy, and flexibility handling.

For quick online docking without local installation, web servers like AutoDock Vina (Webina), SwissDock, and CB-Dock are popular choices. SwissDock is useful for blind docking, while CB-Dock automatically detects binding sites for faster results. HADDOCK is another excellent option, especially when experimental data is available to guide docking. If you prefer a commercial but user-friendly platform, DockingServer provides a simple interface with free limited access.

For more advanced users who need high accuracy and control, standalone tools like AutoDock Vina, AutoDock4, and GOLD are widely used. GOLD is a commercial software known for its precision, while AutoDock Vina is free and efficient for most docking tasks. Glide (Schrödinger) is another industry-standard tool, though it requires a paid license. Open-source alternatives like rDock and LeDock are also available, particularly useful for virtual screening and academic research.

To prepare docking inputs, databases like the Protein Data Bank (PDB) provide protein structures, while PubChem and ZINC offer ligand libraries. The PDBbind database is particularly helpful for benchmarking, as it contains experimentally validated protein-ligand complexes with binding affinity data.

For learning protein-ligand docking, tutorials from AutoDock’s official website, YouTube channels like "Bioinformatics Coach," and books such as Molecular Docking for Computer-Aided Drug Design can be very useful.

If you need a quick and easy solution, web-based tools like SwissDock or CB-Dock are recommended. For high-precision docking, GOLD or Glide are better choices, while free tools like AutoDock Vina and rDock are great for flexibility and academic use.

Shibam Dey -- For molecular docking, you could use the web servers cited by Abdulhamid Dehghani. Alternatively, you could use local installations of AutodDock or Vina. For getting 3D structures of lipids, it should be possible to download 3D SDF files of from PubChem or ChemSpider. Otherwise, you could do 2D to 3D conversions along with energy minimization (geometry optimization) in OpenBabel. Regarding docking, keep in mind that lipid molecules tend to have large numbers of torsions (rotatable bonds), which can yield many different confromations of the ligand poses.