AI-Dock & AI-Dock Plus

AI-Dock

AI-Dock is an innovative docking module that utilizes AI to predict protein-ligand interactions based on binding energy (kcal/mol) and
and improve accuracy through deep learning models.
Predecessor module: PocketFinder

Parameters

Check the docking box

Before you start the docking process, check the docking box.
You can reposition or resize the box.

Docking options

Select a ligand from the ligand library provided by Pharmaco-Net (Ligand Select) or,
upload a ligand file stored on your computer (Ligand Upload) to dock with your target protein.

① Number of Results: Number of binding energy results displayed
By default, displays the top 500 results based on binding energy (adjustable to get all screening results)
② Ligand Select or Ligand Upload:
- Select “Random”, select a library (FDA, Enamine, Mcule, Natural Origin, etc.) and enter the number of ligands to be screened.
- Select “Upload” and upload a zip file containing the ligands to be screened.
③ GPU Threading Count: Number of GPUs to use for docking
By default, 1 thread is used (increasing the number of threads can make the screening process faster)

We recommend keeping the advanced options at their default values to ensure optimal screening process conditions.

① Number of Runs: The number of auto-docking runs.
② Population Size: The number of individuals in the population, where each individual is a combination of a genotype and its associated phenotype.
③ Heuristics: Whether to use heuristic algorithms.
The use of heuristic algorithms in docking allows the structural space to be explored more efficiently and effectively to increase the probability of identifying the best mating structure.
④ RmStol: Root mean square deviation tolerance (unit: angstroms, Å)
Clustering similar ligand conformers based on their RMSD to identify and group the most likely binding modes
⑤ Ligand Types: Types of atoms present in the ligand
⑥ Keep Ligand: Select ligands that the user wants to keep from the original protein file during the docking simulation.

Running AI-Dock module

Progress messages

Module completed

AI-Dock Plus

AI-Dock Plus is an upgraded version of AI-Dock. It is trained with a larger dataset to improve prediction accuracy.
Predecessor modules: PocketFinder, Ligand Library, Ligand Upload

Parameters

Ligand modules

AI-Dock Plus uses a separate module for ligand selection.
- Ligand Library selects ligands from Pharmaco-Net.
- Ligand Upload uploads custom ligands from the user's computer.

💡 Other parameters for running AI-Dock Plus are similar to those for AI-Dock. For more information, see AI-Dock Parameters.