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FireDock specifications

Information


Unique identifier OMICS_03782
Name FireDock
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for FireDock

FireDock in publications

 (28)
PMCID: 5929558
PMID: 29715318
DOI: 10.1371/journal.pone.0196484

[…] algorithm to find docking transformations with good molecular shape complementarity []. scoring and refining of the docked complexes produced by fast rigid-body docking was performed by employing firedock server [,]. complexes with high global docking energy, attractive vander waal energy and hydrogen bonding energy were subjected to molecular dynamics simulation []., a computational systems […]

PMCID: 5729456
PMID: 29237407
DOI: 10.1186/s12881-017-0506-4

[…] topography of proteins (castp) [, ]. docking analysis was carried out using patchdock server [, ]. the refinement of first 10 docked complexes, obtained through patchdock, was carried out using firedock [, ]. representations (2-dimensional) and analysis of protein-ligand interaction complexes was done using ligplot []., though all typical symptoms of the disease were not manifested […]

PMCID: 5635221
PMID: 28777375
DOI: 10.1038/cdd.2017.123

[…] (pdb id: 2yxj) by using the swiss model software (swiss-pdb viewer 4.0.4, http://spdbv.vital-it.ch). the abt-737 was docked into the δn-bcl-xl homology model and the model was refined by using firedock web server. was rendered with ucsf chimera (ucsf chimera-visualization system for exploratory research and analysis)., total rna was extracted from the primary hippocampal neurons by using […]

PMCID: 4837367
PMID: 27094446
DOI: 10.1038/srep24535

[…] to predict the protein–protein interaction site. simultaneously, for protein–protein docking studies, the web version of patchdock was executed and further improvement and ranking was done using firedock. docking studies were done under default complex-type settings using rv3131 model (ligand) and the crystal structure of tlr2 (pdb id: 2z82) was obtained from protein data bank (receptor)., […]

PMCID: 4835421
PMID: 28330175
DOI: 10.1007/s13205-016-0422-x

[…] performed by patch dock server by uploading the structures to web server (schneidman-duhovny et al. ) that works based on shape complementarity principles and again the outcomes were refined with firedock server (andrusier et al. ; mashiach et al. ) that reshuffles the interface side chains and amends the molecule’s relative orientation. analysis of ligand binding interactions and docking […]


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

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