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SnugDock specifications

Information


Unique identifier OMICS_20918
Name SnugDock
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jeffrey Gray <>

Publication for SnugDock

SnugDock in publications

 (8)
PMCID: 5923367
PMID: 29642526
DOI: 10.3390/cancers10040112

[…] the rosetta antibody protocol http://rosie.graylab.jhu.edu/antibody [,,,,]. 72a1 antibody:gp350 dockings were initially aligned using hex 8.0 cuda software [] and further refined using the rosetta snugdock protocol http://rosie.graylab.jhu.edu/snug_dock [,,] or the rosetta docking 2 protocol http://rosie.graylab.jhu.edu/docking2 [,,]. the level of humanization for the hu72a1 vr construct […]

PMCID: 5857718
PMID: 29560474
DOI: 10.1016/j.heliyon.2018.e00564

[…] was examined with epitopia software, whereas allergen properties were tested using algpred. the pattern of the tandem epitope binding with anti-gp350/220 antibodies was performed using z-dock and snugdock. the tandem epitope was then overproduced in e. coli strain bl21 as a host cell., our model demonstrated a successfully designed and overproduced tandem epitope. the tandem epitope […]

PMCID: 5557897
PMID: 28811664
DOI: 10.1038/s41598-017-08414-y

[…] therefore, accurate modeling of the bound structures starting from the unbound structures or homology models is critical for improving accuracy. flexible backbone algorithms such as ensembledock and snugdock based on the conformer selection (cs) binding models previously shown to help improve interface quality of the models generated using unbound and homology complexes can be of immense value. […]

PMCID: 5552345
PMID: 28759640
DOI: 10.1371/journal.ppat.1006469

[…] modeling of ab-ag interactions has advanced considerably in recent years and several examples of complexes with close to atomic accuracy have been reported in the literature []. using the snugdock protein-protein docking algorithm [], we obtained an initial model for binding of the peptide to the cdr region of the 2a10 fab fragment (). we then performed, in triplicate, three 50 ns md […]

PMCID: 4575156
PMID: 26381271
DOI: 10.1371/journal.pone.0138220

[…] for some particularly useful or common cases, a number of “remix protocols” have been developed. notable examples include: fold and dock[], which combines symmetric docking with ab initio folding; snugdock[], which combines loop modeling with multibody docking; and rosettaremodel[], which seeks to unify a large number of design-relevant sampling algorithms under one interface. as the number […]


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SnugDock institution(s)
Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Program in Molecular & Computational Biophysics, Johns Hopkins University, Baltimore, MD, USA
SnugDock funding source(s)
Supported by National Institute of Health (R01-GM078221) and UCB S. A.

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