There are many online docking servers and you can try any of those

• HEX
• GrammX
• Haddock

i recommend only 1....autodock vina

There are several web servers that make molecular docking quick and easy without the hassle of local installations.

If you want a straightforward, user-friendly, and web-based solution to quickly test your protein-ligand interactions, you can try our online docking platform: Molecular Docking Online. It is designed precisely for rapid screening and ease of use.

Alternatively, depending on your specific needs, here are a few other widely used and reliable online servers:

SwissDock: A very popular web server based on the EADOCK DSS engine, great for filling simple docking needs.

CB-Dock2: Excellent if you don't know the exact binding cavity, as it automatically predicts cavities and performs blind docking using AutoDock Vina.

HDOCK: If you ever need to pivot to protein-protein docking rather than small molecules, this is a fantastic automated server.

If you just need a quick validation for your protein and small molecule, give our tool a spin! Let me know if you run into any issues with the formats or parameters.

For a protein structure plus a small molecule, the usual quick-and-dirty choice is still AutoDock Vina or a Vina-based web server. The important distinction is that some older answers here list protein-protein docking servers, which are not necessarily the right tool for a small-molecule ligand.

A practical decision path:

1. If you know the binding site, use AutoDock Vina, SMINA, GNINA, or a web server that lets you define the search box. This is usually the fastest route for a small molecule.
2. If you do not know the binding site, use a blind-docking or cavity-detection workflow, for example CB-Dock2/Vina-style cavity docking, then inspect the top poses carefully.
3. If the "small molecule" is really a peptide, RNA, DNA, or another protein, do not force it into a standard Vina workflow. Use a method intended for that partner type, such as HADDOCK/LightDock/HDOCK depending on the case.

For a minimal Vina-style run, you need:

• a cleaned receptor structure, usually PDB converted/prepared to PDBQT,
• a ligand with sensible bond orders, protonation, 3D coordinates, and PDBQT atom types,
• a search box centered on the pocket,
• and enough exhaustiveness to make the result reproducible enough for a first pass.

The quick sanity checks are more important than the exact interface you use: make sure the ligand is in the pocket you intended, check for obvious clashes, compare several poses rather than only the top score, and avoid treating the docking score as an experimental binding affinity. Docking is useful for generating hypotheses and ranking poses, not proving activity by itself.

If setup/file handling is the main blocker, I work on ProteinIQ's AutoDock Vina tool, which runs this kind of small-molecule Vina workflow in the browser. But the same caveat applies there too: the result is only as good as the receptor preparation, ligand state, and search box.