Fast and accurate protein substructure searching with simulated annealing and GPUs

Software

Source code and executables (Linux x86_64, NVIDIA CUDA and the CUDA Toolkit must be installed to use the GPU implementation for NVIDIA GPUs): cuda_satabsearch.tar.gz.

Versions built for 32 bit systems: cuda_satabsearch_32.tar.gz (32-bit CUDA 2.3), cuda_satabsearch_32_cudav3.tar.gz (32-bit CUDA 3.0).

You can still get the source code and tableaux databases from the old site http://munk.cis.unimelb.edu.au/~stivalaa/satabsearch/ (which, however, I can no longer update), and the source code from GitHub.

This software can be used freely for any purpose, modified, redistributed, etc. with no restrictions, except where noted that NVIDIA SDK sample code is used by "This software contains source code provided by NVIDIA Corporation.", namely, for the Mersenne Twister pseudorandom number generator. In this case the only restriction is that the preceding NVIDIA statement is retained (as it is here and in comments in the relevant code fragments), as specified in the NVIDIA CUDA SDK End User License Agreement. However we would appreciate it if you acknowledge your use of it, and in particular if you would cite our paper in any publication that makes use of it.

CUDA 5.0 implementation

(New, as of November 2013).

SA Tableau Search was originally developed on CUDA 2.3, which did not even have a device pseudorandom number generator library, so the Mersenne Twister example from the SDK was adapted to provide a RNG on the device. Later versions provide the CURAND library, and CUDA 5.0 changed some APIs, so the code has been updated to run on more modern GPUs with CUDA 5.0. The following source code (and compiled executable) was built and tested on a 64-bit Linux system with CUDA 5.0.35 and a Tesla M2070 GPU:

cuda_satabsearch_64_cudav5.tar.gz

This software can be used freely for any purpose, modified, redistributed, etc. with no restrictions. However we would appreciate it if you acknowledge your use of it, and in particular if you would cite our paper in any publication that makes use of it.

Web server

SA Tableau Search is also available for online use via the Pro-origami web server. However, the server is does not have a GPU, so SA Tableau Search runs on the server CPU and is therefore orders of magnitude slower than running on a modern GPU.

Tableaux database

The tableaux database was built with buildtableauxdb.py -t dssp -3 -5 -p none The distance matrices were built with buildtableauxdb.py -t dssp -3 -5 -p none -d and the combined tableaux and distance matrix database in ASCII format created with the convdb2.py script, and sorted by size with the sort_tableux_db_pbs_script.sh script. These scripts are included in the scripts.tar.gz file.

Combined tableau and distance matrix database for ASTRAL SCOP 1.75 95% sequence identity subset, sorted by size

The list of queries in the 200 query set is query200-1.75.list.

Reference

If you use our software, data, or results in your research, please cite:

Stivala, A., Stuckey, P., Wirth, A., Fast and accurate protein substructure searching with simulated annealing and GPUs BMC Bioinformatics 2010, 11:446

Contact

Alex Stivala