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FiberDock specifications

Information


Unique identifier OMICS_03781
Name FiberDock
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for FiberDock

FiberDock in publications

 (20)
PMCID: 5840830
PMID: 29510668
DOI: 10.1186/s12859-018-2105-6

[…] protocol uses this information to infer interaction between a pair of target proteins. in the end, a predicted protein complex is subjected to flexible refinement and energy minimization using the fiberdock [] tool []. the generated complexes are ranked according to the global energy binding score, and they are selected if they have a score equal to or less than 0. this threshold […]

PMCID: 5543104
PMID: 28775330
DOI: 10.1038/s41598-017-07351-0

[…] and making sure that at least one hotspot at each side is conserved, prism transforms the surfaces to the template interface to form a protein complex in the third step. finally, in the last step, fiberdock, is used for flexible refinement of the complexes and ranking them based on the binding energy scores. fiberdock models both backbone and side-chain flexibility. the current prism […]

PMCID: 5870628
PMID: 28881968
DOI: 10.1093/bioinformatics/btx233

[…] first tbd methods, which is based on an underlying interface database was prism (). in its recent version (), prism is based on two algorithms, which have been developed in our lab, multiprot () and fiberdock (). for each interface in the template database of prism multiprot is used to structurally align the target proteins to both sides of the interface. the resulting modelled interfaces, […]

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

[…] structural alignments, and machine learning to predict interfacial residues for a target protein. the top 10 models selected by erankppi are finally subjected to a flexible refinement with fiberdock []. fiberdock mimics the induced fit by accounting for both side-chain and backbone flexibility. the side-chain flexibility is modeled using a rotamer library, whereas a normal mode […]

PMCID: 5261736
PMID: 28118389
DOI: 10.1371/journal.pone.0170625

[…] knowledge-based scoring functions for each class of ligands or step in the protocol[][][]., composite scoring functions such as pydock [], rosettadock [], haddock [], zdock [][], firedock [], and fiberdock [] usually use a linear combination of scoring terms to further improve their scoring by accounting for independent complex features. the linear weights for this purpose are determined […]


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FiberDock institution(s)
Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel

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