FlexPepDock specifications

Information


Unique identifier OMICS_05698
Name FlexPepDock
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for FlexPepDock

FlexPepDock in publications

 (45)
PMCID: 5913127
PMID: 29686315
DOI: 10.1038/s41598-018-24501-0

[…] for binding that can be recapitulated using modeling tools.figure 7, we also used computational docking to analyze the binding energy landscapes of the fab/aβ complexes. in brief, we first used flexpepdock to generate additional docking models for each of the fab/aβ complexes. figure  shows a sample of the many different conformations adopted by the aβ peptide when interacting […]

PMCID: 5897774
PMID: 29510984
DOI: 10.15252/embj.201797902

[…] whether a single molecule of tacc3 could span both the docking site 1 and the substrate binding site of aurora‐a. to address this point, we generated a model of tacc3 bound to active aurora‐a using flexpepdock server (raveh et al, ; london et al, ) and the structure of an active aurora‐a, phosphorylated on thr288 in complex with tpx2 (fig g). the surface of aurora‐a in the vicinity of the tacc3 […]

PMCID: 5802825
PMID: 29410427
DOI: 10.1038/s41467-017-02578-x

[…] and mutational data described above were next used to produce an in silico model of cegc3-interaction with dotm153, using the docking server cabs, and subsequently refining the resulting model using flexpepdock,, a rosetta-based server. the final model suggests that cegc3 is primarily helical. binding is observed between the main middle glu-rich helical motif of cegc3 (residues e155, e158, […]

PMCID: 5792643
PMID: 29386631
DOI: 10.1038/s41598-018-20290-8

[…] although molecular modeling of disordered proteins has its difficulties, as traditional rigid-body in silico docking methods cannot sufficiently account for the more extensive protein dynamics, the flexpepdock webserver provides a freely available docking methodology whereby only one molecule is portrayed as rigid and an approximate peptide structure of up to 30 residues can be docked […]

PMCID: 5772351
PMID: 29343728
DOI: 10.1038/s41467-017-02746-z

[…] k102e mutant and on the local sampling of the region surrounding the mutated residue., the modelling of the oligomers was done in ucsf chimera. the positions of the 102–125 loops were refined using flexpepdock monte carlo approach. the figure has been generated using ucsf chimera., intracellular aggregates of p62 were scored by eye; the scorer was blinded to the cell treatment and the specific […]


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FlexPepDock institution(s)
Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University, Jerusalem, Israel

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