sharpdock 1.0.0

Automated focused molecular docking pipeline for Autodock Vina

SHARPDOCK v1.0.0

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An Integrated Pipeline for Focused Molecular Docking
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SHARPDOCK is a tool, designed for Automated Focused Molecular Docking. It handles the calculating grid box coordinates based on specific amino acid residues to parallelizing ligand preparation and executing AutoDock Vina.

For more tools visit: https://github.com/alpha-horizon

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Features

• Grid Calculation: Automatically centers and sizes the docking box based on a user-provided list of active site residues.

• Parallel Processing: Prepare multiple ligands simultaneously, Can handle ligands in 2D/3D format.

• Summary: Outputs a sorted CSV of binding affinities and organized docking poses.

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Input Requirements

1. Receptor (-r)

   Format: .pdb

   NOTE: Ensure the protein structure is clean (remove non-essential waters or ions).

2. Ligands (-l)

   Format: .sdf (2D/3D)

   NOTE: Place all ligand files in a single directory.

3. Active Site Specification (-s)

   Use the following format:

   "ChainID:ResidueID ResidueID; ChainID:ResidueID"

   Example: "A:101 102 105; B:45" (This focuses the docking on residues 101, 102, and 105 of Chain A, and residue 45 of Chain B).

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pip Installation

To install SHARPDOCK, you can use the command mentioned below.

    pip install sharpdock

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Command Line Usage

This tool supports full argument-based execution for automation and pipelines:

    sharpdock --receptor receptor.pdb --sites "A:101 102; B:70" --ligands ./my_ligands --output results

Options:

    -r	--receptor       Path to receptor PDB file	
    -s	--sites	         Active site residues (e.g., 'A:10 11; B:50')	
    -l	--ligands	     Folder containing ligand .sdf files |ligands (default)|
    -o	--output	     Output directory name |sharpdock_results (default)|
    -p	--padding	     Grid box padding in Angstroms (Å) |5.0 (default)|
    -e	--exhaustiveness Vina search exhaustiveness |32 (default)|

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Directory Structure

SHARPDOCK organizes your results automatically:

• final_results.csv: A ranked list of ligands and their best binding affinities (kcal/mol).

• docking_outputs/: Contains the .pdbqt files of the docked poses.

• ligands_pdbqt/: The prepared and optimized ligand files.

• box_config.txt: The exact grid coordinates used for the Vina run.

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Contribution

For more tools or to report issues, visit the official GitHub repository:

GitHub: https://github.com/alpha-horizon

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