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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 GPL v2 and GNU LGPL v2.1 licenses. See details.

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"
}

A full list of publications is available here.

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: diogom@scripps.edu
• Leonardo Solis-Vasquez: solis@esa.tu-darmstadt.de