FTDock specifications

Information


Unique identifier OMICS_08541
Name FTDock
Alternative name Fourier Transform rigid-body Docking
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Publication for Fourier Transform rigid-body Docking

FTDock in publications

 (26)
PMCID: 5935668
PMID: 29728612
DOI: 10.1038/s41598-018-25279-x

[…] of these peptides with bmp-2 and bmp-2 receptor (type ia and activin receptor type 2 a). the bmp-2 and bmp-2 receptor structures are from pdb ids 1rew and 2goo and the programs zdock and ftdock were used for the protein-protein docking., all sample conditions were analyzed in triplicates and compared using one-way anova with post-hoc tukey-kramer using instat software (graphpad). […]

PMCID: 5484654
PMID: 28653156
DOI: 10.1007/s40203-017-0023-3

[…] compound (ligand) to bind with a target protein (e.g. receptor) to form a stable complex. several tools can be used for molecular docking methods such as argusdock, dock, fred, ehits, auto dock and ftdock. the ability of a ligand to binds with the active site of a receptor is then tested to assess the activation or inhibition strength (pedro and lei )., based on the facts above, this study aims […]

PMCID: 5334405
PMID: 28317012
DOI: 10.1007/s41048-017-0034-y

[…] in the following, we give a detailed description of the usage of 3drpc., rpdock is a fft-based, rigid-body sampling method. the overall process of rpdock resembles protein–protein docking algorithm ftdock (gabb et al. ). first, the protein is discretized into three-dimensional grid and the rna is rotated by euler angles and then discretized into three-dimensional grid. next, a full translation […]

PMCID: 5293240
PMID: 28166227
DOI: 10.1371/journal.pone.0169356

[…] our method, we used the set of intra-molecular protein complexes from [], using three-fold cross-validation. for each protein complex in the data set, 10,000 docking decoys were generated using the ftdock docking software [] using the bound protein structures, with the electrostatic correlation score as a binary filter to avoid decoys with unfavourable electrostatic interactions. only protein […]

PMCID: 4839147
PMID: 27103992
DOI: 10.1186/s13628-016-0029-y

[…] in a study performed similarly to ours, the unres coarse-grained force field was tested as rescoring function []. the number of hits that were retained in the top-10 predictions generated by ftdock [] decreased by more than 50 %, while with our approach the success rate decreases by only 1–2 % at npred=10. this shows that while opep is still not a perfect scoring function […]


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FTDock institution(s)
Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, Lincoln's Inn Fields, London, UK

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