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MEGADOCK-GPU
A fast protein-protein docking software on GPUs.
MEGADOCK-GPU version 1.0 was integrated to current version (ver. 4.0).
http://www.bi.cs.titech.ac.jp/megadock/
Download
Ver. 1.0: megadock-gpu-1.0.tgz
Requirements
MEGADOCK-GPU requires nVIDIA's GPUs which are capable for CUDA and the following libraries.
Installation
Extract tarball contents
$ tar xzf megadock-gpu-1.0.tgz
$ cd megadock-gpu-1.0
Edit Makefile
- Add your C++ compiler to the CC line
(ex. CC = icpc -openmp)
- Add the path to your FFTW header files to the CFLAGS line
(ex. CFLAGS = -c -I/usr/local/include)
- Add the path to your installation of FFTW library to the LDFLAGS line
(ex. LDFLAGS = -lm -L/usr/local/lib -lfftw3f)
- Add the path to your installation of CUDA to the ROOTDIR line
(ex. ROOTDIR = /opt/cuda/5.0/samples/)
Usage
Example:
$ ./megadock-gpu -R receptor.pdb -L ligand.pdb -o dock
$ perl create.pl dock.out
Attention:
receptor.pdb, ligand.pdb and create_lig must be in your current
directory when you try to create all predicted structures using create.pl.
Options:
-R filename : receptor pdb file
-L filename : ligand pdb file
-o filename : set the output filename (default to "$R-$L.out")
-O : output the detail file named "[filename].detail" (default to none)
-N integer : set the number of output predictions (default to 2000)
-t integer : set the number of predictions per each rotation (default to 1)
-F integer : set the number of FFT point (default to none)
-v float : set the voxel size (default to 1.2)
-D : use 6 degree rotation (54000 rotations) instead of 15 degree (3600 rotations)
-e float : set the electrostatics term ratio (default to 1.0)
-d float : set the hydrophobic term ratio (default to 1.0)
-a float : set the rPSC receptor core penalty (default to -45.0)
-b float : set the rPSC ligand core penalty (default to 1.0)
-f 1/2/3 : set function
(1: rPSC, 2: rPSC+Elec, 3: rPSC+Elec+Hydrophobic, default to 3)
-h : show the help messeage
Thread parallelization:
MEGADOCK can parallelize rotation calculations by using OpenMP.
You can tell MEGADOCK the number of OpenMP threads you want to use by
environmental variable such as $OMP_NUM_THREADS.
About post process and interaction prediction
- You need to run ZRANK on your docking output. ZRANK is available at:
http://zlab.bu.edu/zdock/
Reference: Pierce B and Weng Z.,
A combination of rescoring and refinement significantly improves protein docking performance.,
Proteins, 72(1):270-279, 2008.
[Paper]
- Details on clustering and interaction prediction method, see:
Matsuzaki Y, Matsuzaki Y, Sato T, Akiyama Y.,
In silico screening of protein-protein interactions with all-to-all rigid docking and clustering:
an application to pathway analysis.,
J Bioinform Comput Biol, 7(6):991-1012, 2009.
[Paper]
References
- Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue, Yutaka Akiyama. MEGADOCK-GPU: An accelerated protein-protein docking calculation on GPUs, Parallel and Cloud-based Bioinformatics and Biomedicine, 2013. (accepted)
- Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama. MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data, Protein and Peptide Letters, XX(XX), XX-XX, 2013. (in press)
- Masahito Ohue, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama. Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: an Application to Interaction Pathway Analysis. Lecture Note in Bioinformatics 7632 (In Proc. of PRIB 2012), 178-187, Springer Heidelberg, 2012.
SpringerLink
- Masahito Ohue, Yuri Matsuzaki, Yutaka Akiyama. Docking-calculation-based Method for Predicting Protein-RNA Interactions. Genome Informatics, 25(1), 25-39, 2011.
Copyright © 2013 Akiyama Laboratory, Tokyo Institute of Technology, All Rights Reserved.
Last update : 2013/6/3