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