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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 in publications

 (5)
PMCID: 5840830
PMID: 29510668
DOI: 10.1186/s12859-018-2105-6

[…] protein models of each group were applied to two docking methodologies: first template-based docking through the prism protocol [] tool, and second, the rigid-body docking through the megadock [] tool version 4.0.2., the prism protocol requires as input atomic coordinates of two proteins, and a template set formed by pairs of proteins that are known to interact. this tool applies […]

PMCID: 5751226
PMID: 29206185
DOI: 10.3390/ijms18122623

[…] 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 […]

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

[…] []., 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 […]

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

[…] 5.0 []. these proteins, used as docking receptors, interacted with multiple true partners, as described in . to generate decoy sets, rigid-body docking was performed for each docking receptor using megadock ver. 4.0 [], and proteins were docked with 44 different ligand proteins, including their true partners. we then introduced the concept of broad interaction profiles (bips), which were made […]

PMCID: 4044902
PMID: 24564962
DOI: 10.1186/1753-6561-7-S7-S6

[…] the human apoptosis signaling pathway, we obtained a precision value of 0.333, which is higher than that achieved using conventional methods (0.231 for prism, a template-based method, and 0.145 for megadock, a non-template-based method), while maintaining an f-measure value (0.285) comparable to that obtained using conventional methods (0.296 for prism, and 0.220 for megadock)., our consensus […]


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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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