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Citations per year

Number of citations per year for the bioinformatics software tool FTDock
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This map represents all the scientific publications referring to FTDock per scientific context
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Protocols

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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No version available

Publication for Fourier Transform rigid-body Docking

FTDock citations

 (26)
library_books

Identification of the effector domain of biglycan that facilitates BMP 2 osteogenic function

2018
Sci Rep
PMCID: 5935668
PMID: 29728612
DOI: 10.1038/s41598-018-25279-x

[…] interactions 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. […]

library_books

Using 3dRPC for RNA–protein complex structure prediction

2017
Biophysics Rep
PMCID: 5334405
PMID: 28317012
DOI: 10.1007/s41048-017-0034-y

[…] 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 s […]

library_books

Improving protein protein interaction prediction using evolutionary information from low quality MSAs

2017
PLoS One
PMCID: 5293240
PMID: 28166227
DOI: 10.1371/journal.pone.0169356

[…] k 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 co […]

library_books

Evaluation of the coarse grained OPEP force field for protein protein docking

2016
BMC Biophys
PMCID: 4839147
PMID: 27103992
DOI: 10.1186/s13628-016-0029-y

[…] oreover, 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 for protein-prot […]

library_books

Computational Prediction of RNA Binding Proteins and Binding Sites

2015
Int J Mol Sci
PMCID: 4661811
PMID: 26540053
DOI: 10.3390/ijms161125952

[…] c RNA–protein docking method exists []. Several protein–protein docking programs accept RNA and protein coordinates as inputs to generate RBPs, such as HADDOCK [], GRAMM [], HEX [], PatchDock [], and FTDock []. The above strategies for RNA-binding site and RBP prediction are summarized in .Although the methodology for predicting protein–protein interactions and protein–DNA interactions are well es […]

library_books

Molecular features of interaction between VEGFA and anti angiogenic drugs used in retinal diseases: a computational approach

2015
Front Pharmacol
PMCID: 4624855
PMID: 26578958
DOI: 10.3389/fphar.2015.00248

[…] VEGFR1d2_R2d3 structural optimization, the protein-protein docking of VEGFR1d2_R2d3 was also carried out using its starting model.Given the 3D coordinates of two interacting proteins, pyDockWEB uses FTDock for generation of the predicted complexes by rigid-body docking (Gabb et al., ). No restrains have been applied in this stage. The predicted complexes were then evaluated by PyDock scoring func […]


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

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