F2Dock statistics

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Citations per year

Number of citations per year for the bioinformatics software tool F2Dock
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Tool usage distribution map

This map represents all the scientific publications referring to F2Dock per scientific context
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F2Dock specifications

Information


Unique identifier OMICS_03786
Name F2Dock
Alternative name Fast Fourier Protein-Protein Docking
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data Receptor and ligand files
Input format PDB
Output data Individual conformations, breakdown of scores of different terms, statistics, smooth/UofB rendering of the complex, overlayed rendering of multiple conformations
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Fast Fourier Protein-Protein Docking

F2Dock citations

 (3)
library_books

X ray, Cryo EM, and computationally predicted protein structures used in integrative modeling of HIV Env glycoprotein gp120 in complex with CD4 and 17b

2016
PMCID: 4749890
PMID: 26937457
DOI: 10.1016/j.dib.2016.01.001

[…] The binding site analysis was performed by docking CD4 and 17b with the optimized models using F2Dock . F2Dock reports the top 1000 possible binding poses. We define the parts of the surface of gp120 that is in contact with the CDR loops of CD4 and 17b in a docking pose as the footprint/site of […]

library_books

IFACEwat: the interfacial water implemented re ranking algorithm to improve the discrimination of near native structures for protein rigid docking

2014
BMC Bioinformatics
PMCID: 4290663
PMID: 25521441
DOI: 10.1186/1471-2105-15-S16-S9

[…] ranking technique ZRANK, the IFACEwat obtained success rates of 92.3% (8% better) and 90% (5% better) respectively for medium and difficult cases. When comparing with the current re-ranking method in F2Dock, which employs a Generalized Born (GB) model in its energy-based function, it was shown that the IFACEwat performed equivalently with or even better than the GB-rerank F2Dock, especially for th […]

library_books

Protein Protein Docking with F2Dock 2.0 and GB Rerank

2013
PLoS One
PMCID: 3590208
PMID: 23483883
DOI: 10.1371/journal.pone.0051307

[…] F2Dock takes two PDB files as inputs. First the PDB files are processed by PDB2PQR where missing atoms such as Hydrogens are added, the protein is optimized for hydrogen bonding, and charge and radiu […]


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F2Dock institution(s)
Computational Visualization Center, Department of Computer Sciences and The Institute of Computational Engineering and Sciences, The University of Texas, Austin, TX, USA; Google Inc; Mountain View, CA, USA
F2Dock funding source(s)
This work was supported in part by NSF grants IIS-0325550, CNS-0540033 and grants from the NIH R01 GM074258, R01-GM073087, R01-EB004873.

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