https://github.com/l30nardosv/reproduce-ia3-moleculardocking

Reproducing IA^3 2020 Paper: "Parallelizing Irregular Computations for Molecular Docking"
https://github.com/l30nardosv/reproduce-ia3-moleculardocking

autodock-gpu cpu gpu molecular-docking molecular-docking-scripts opencl paper reproducible-research

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Reproducing IA^3 2020 Paper: "Parallelizing Irregular Computations for Molecular Docking"

• Host: GitHub
• URL: https://github.com/l30nardosv/reproduce-ia3-moleculardocking
• Owner: L30nardoSV
• License: cc0-1.0
• Created: 2020-10-08T14:12:08.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2022-01-07T17:03:29.000Z (about 3 years ago)
• Last Synced: 2023-06-05T15:35:28.505Z (over 1 year ago)
• Topics: autodock-gpu, cpu, gpu, molecular-docking, molecular-docking-scripts, opencl, paper, reproducible-research
• Language: Shell
• Homepage:
• Size: 293 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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[![DOI](https://zenodo.org/badge/302362741.svg)](https://zenodo.org/badge/latestdoi/302362741)

# Reproducing IA^3 2020 Paper: _Parallelizing Irregular Computations for Molecular Docking_

This repository contains the scripts and configuration files used in the _Artifact Appendix_ of the article accepted at: 

[The 10th Workshop on Irregular Applications: Architectures and Algorithms (IA^3), 2020](https://hpc.pnl.gov/IA3/IA3/IA3-2020/index.html)

and published on IEEExplore: 

https://doi.org/10.1109/IA351965.2020.00008.

## Contents

* Scripts for re-running experiments described in paper

	* See bash scripts withtin root folder

* Additional files containing parameters for AutoDock

	* See [docking parameter files](./dpf_autodock426) folder

* Output examples of both AutoDock and AutoDock-GPU

	* See [docking log](./dlg_examples) folder

## Downloads

Required programs and inputs:

* AutoDock-GPU

	*  https://github.com/ccsb-scripps/AutoDock-GPU

* Data set

	* URL: https://doi.org/10.5281/zenodo.4031961

	* DOI: `10.5281/zenodo.4031961`

## Further information

Additional material include the [paper preprint](https://www.esa.informatik.tu-darmstadt.de/assets/publications/materials/2020/2020_IA3_LVS.pdf) and [presentation slides](https://www.esa.informatik.tu-darmstadt.de/assets/publications/materials/2020/2020_IA3_LVS_slides.pdf).