Home

About

Welcome to the AutoDock-GPU wiki!

AutoDock-GPU is an OpenCL implementation of AutoDock LGA.

Main project is hosted under: https://ccsb.scripps.edu/autodock

Features

AutoDock-GPU leverages the embarrassingly parallelism of AutoDock LGA, by processing ligand-receptor poses in parallel over multiple compute units on a GPU device.

Besides the legacy Solis-Wets local search method, AutoDock-GPU adds newly implemented local-search methods based on gradients of the scoring function.

One of these methods, ADADELTA, has proven to increase significantly the docking quality in terms of scores and RMSDs.

License

AutoDock-GPU is released under the GNU GPLv2 license.

Guidelines

• Users
• Developers

Citation

A paper describing the OpenCL implementation and evaluation of AutoDock-GPU was uploaded as a preprint in ChemRXiv.

If you find AutoDock-GPU useful for your work, please cite it as:

@article{AutoDock-GPU,
author = "Santos-Martins, Diogo and Solis-Vasquez, Leonardo and Koch, Andreas and Forli, Stefano",
title  = "{Accelerating AutoDock4 with GPUs and Gradient-Based Local Search}",
year   = "2019",
month  = "8",
url    = "https://chemrxiv.org/articles/Accelerating_AutoDock4_with_GPUs_and_Gradient-Based_Local_Search/9702389",
doi    = "10.26434/chemrxiv.9702389.v1"
}

Support

If you encounter any issues or have any questions, please use any of the following:

• The GitHub issues page: https://github.com/ccsb-scripps/AutoDock-GPU/issues
• The AutoDock4 mailing list: http://autodock.scripps.edu/mailing_list

You can also contact the main developers via email:

• Diogo Santos-Martins: [email protected]
• Leonardo Solis-Vasquez: [email protected]