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MEGADOCK specifications

Information


Unique identifier OMICS_05456
Name MEGADOCK
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C++
Parallelization CUDA
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for MEGADOCK

MEGADOCK citations

 (11)
library_books

Building protein protein interaction networks for Leishmania species through protein structural information

2018
BMC Bioinformatics
PMCID: 5840830
PMID: 29510668
DOI: 10.1186/s12859-018-2105-6

[…] d they are selected if they have a score equal to or less than 0. This threshold is the same one used by the developers of the tool to predict interactions in the Prism Web Server [].In parallel, the Megadock tool uses only the atomic coordinates of two proteins, and considering shape complementarity, electrostatic and hydrophobic interactions, it computes a set of interaction solutions for a cand […]

library_books

The binding structure and affinity of photodamaged duplex DNA with members of the photolyase/cryptochrome family: A computational study

2018
Biophys Physicobiol
PMCID: 5812317
PMID: 29450111
DOI: 10.2142/biophysico.15.0_18

[…] To model a CRY-DASH complex with damaged dsDNA, we performed the docking simulation using MEGADOCK [,]. In , the docking calculation scheme is shown. Here, in our docking simulation using MEGADOCK, we adopted a default parameter set. Among 2000 snapshots, the structure with the best score […]

library_books

Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures

2017
Int J Mol Sci
PMCID: 5751226
PMID: 29206185
DOI: 10.3390/ijms18122623

[…] akes approximately 15 s, which is up to two orders of magnitude faster than conventional FFT based docking approaches using comparable resolution and scoring functions [] such as GRAMM-X, FRODOCK and MEGADOCK.MEGADOCK [] uses a Katchalski–Katzir algorithm [] and searches probable docking structures in a grid-based 3D space using FFT. MEGADOCK employs a scoring function in which only shape compleme […]

library_books

Across proteome modeling of dimer structures for the bottom up assembly of protein protein interaction networks

2017
BMC Bioinformatics
PMCID: 5427563
PMID: 28499419
DOI: 10.1186/s12859-017-1675-z

[…] reported [].Another study attempted to predict the protein-protein interaction network of the bacterial chemotaxis signaling pathway using an all-to-all docking approach []. Here, two docking tools, MEGADOCK [] and ZDOCK [], were employed to conduct rigid-body docking of all possible combinations of 101 proteins belonging to 13 families, which are known to be part of the chemotaxis signaling path […]

library_books

Specificity of broad protein interaction surfaces for proteins with multiple binding partners

2016
Biophys Physicobiol
PMCID: 5042157
PMID: 27924264
DOI: 10.2142/biophysico.13.0_105

[…] For obtaining decoy sets, we performed docking processes using MEGADOCK ver. 4.0, an FFT-grid-based exhaustive rigid-body docking tool with multiparallel calculations [,]. In this work, docking processes were performed on an Intel Xeon E7-4870 CPU (2.4 GHz, 10 co […]

library_books

Protein protein docking on hardware accelerators: comparison of GPU and MIC architectures

2015
BMC Syst Biol
PMCID: 4331681
PMID: 25707855
DOI: 10.1186/1752-0509-9-S1-S6

[…] change the source code of existing applications if the program is parallelized using OpenMP.We accelerated protein-protein docking calculations by utilizing MIC in both the offload and native modes. MEGADOCK has already been parallelized by looping the rotational angles of the ligand protein using OpenMP and it can be run in parallel on a multi-core CPU. Thus, the native mode implementation paral […]

Citations

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MEGADOCK institution(s)
Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan, Japan; Society for the Promotion of Science (JSPS) and Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan

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