An Ultrafast Pre-screening Method Based on Compound Decomposition
Spresso (Speedy PRE-Screening method with Segmented cOmpounds) is a novel structure-based virtual screening method based on compound decomposition. Partial structures (fragments) are often common among several compounds; therefore, the number of fragment variations neededfor evaluation is smaller than that of compounds. Our method increased calculation speeds up to approximately 200-fold compared to conventional methods.
spresso_decomp_v1.0.3.tar.gz (version 1.0.3, Last update: Mar. 31 2017)
fragment_docking.py (version 1.0.2, Last update: July 8 2016)
calc_compound_score.py (version 1.0.2, Last update: July 8 2016)
Codes are written in C++ and python2.
$ sudo apt-get install libboost-all-dev
$ sudo apt-get install libopenbabel-dev
# Assumed environment is Anaconda # numpy was already installed as a default. $ conda install --channel https://conda.anaconda.org/Clyde_Fare openbabel
$ tar -zxvf spresso_decomp_v1.0.tar.gz $ cd spresso_decomp_v1.0 $ make -j # If it is finished correctly, an executable file "spresso_decompose" is made.
$ ./spresso_decomp -c config.in $ ./spresso_decomp -l ligandfile -f fragmentfile -o annotated_ligandfile
A sample of config.in is here.
$ python fragment_docking.py -g glide_protein_grid.zip -i fragment.sdf -o output.sdf -m SP
$ python calc_compound_score.py annotated_ligand.sdf docked_fragment.sdf scored_ligand.sdf
For each program, "--help" option will tell you further information.
yanagisawa [at] bi.c.titech.ac.jp (Keisuke Yanagisawa, Tokyo Institute of Technology)
Keisuke Yanagisawa, Shunta Komine, Shogo D. Suzuki, Masahito Ohue, Takashi Ishida, Yutaka Akiyama. Spresso: an ultrafast compound pre-screening method based on compound decomposition, Bioinformatics, 33(23): 3836-3843, 2017. doi:10.1093/bioinformatics/btx178 [open access]