sharpdock 2.0.0

Automated focused molecular docking pipeline for Autodock Vina

SHARPDOCK v2.0.0

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An Integrated Pipeline for Focused Molecular Docking
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SHARPDOCK is a high-throughput, automated pipeline for focused molecular docking. It handles the ranking of ligands based on binding affinities by automating grid box generation, receptor/ligand preparation, and parallelized docking execution using AutoDock Vina.

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

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Features

• Automated Grid Box Calculation: No more manual coordinate entry; define sites by chain and residue ID.

• Parallel Ligand Preparation: Process large libraries of ligands in .sdf format.

• Vina Integration: Seamlessly communicates with AutoDock Vina for industry-standard accuracy.

• Formatted Reporting: Generates publication-ready CSVs and detailed log reports.

• Top-Hit Extraction: Automatically isolates the most promising leads for downstream analysis.

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Input Requirements

1. Receptor File (-r / --receptor)

   Format: Standard .pdb file. Note: It is recommended to remove water molecules, ions, and co-crystallized ligands from the PDB file before running the pipeline to prevent interference with the grid box calculation.

2. Ligand Files (-l / --ligands)

   Format: .sdf (Structure Data File). Note: You can input ligands in 2D or 3D structure.

3. Active Site Specification (-s / --sites)

   The site string is the most critical input for Focused Docking. Use the following syntax:

   Single Chain: "A:101 102 105"

   Multiple Chains: "A:101 102; B:70 71"

   Format: ChainID:ResidueID ResidueID; ChainID:ResidueID

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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 -r receptor.pdb -s "A:101 102; B:70" -l ./ligands -n 10

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)|
    -n	--top_hits	Number of top ligands to export	|10 (default)|

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Directory Structure

• After execution, the output folder contains:

• top_hits/: The best-scoring docked poses.

• docking_results.csv: Comprehensive spreadsheet of all scores.

• binding_affinities.log: A human-readable summary of the run parameters and results.

• receptor.box.txt: The specific Vina configuration used for the grid.

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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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