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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

Versioning


No version available

Maintainer


  • person_outline Jeffrey Gray

Publication for SnugDock

SnugDock citations

 (9)
library_books

Construction and Characterization of a Humanized Anti Epstein Barr Virus gp350 Antibody with Neutralizing Activity in Cell Culture

2018
PMCID: 5923367
PMID: 29642526
DOI: 10.3390/cancers10040112

[…] by 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 was as […]

library_books

Designing and overproducing a tandem epitope of gp350/220 that shows a potential to become an EBV vaccine

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

[…] blind docking between ligand (antibody) and receptor (tandem epitope and whole protein gp350/220) via Z-dock software . Resulting docking data were then adjusted according to binding of antigens via snugDock software . Following, bonding patterns between tandem epitopes and antibodies were then compared to bonding patterns between whole protein gp350/220 and antibodies. These bonding patterns are […]

library_books

Structure based cross docking analysis of antibody–antigen interactions

2017
Sci Rep
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. H […]

library_books

T dependent B cell responses to Plasmodium induce antibodies that form a high avidity multivalent complex with the circumsporozoite protein

2017
PLoS Pathog
PMCID: 5552345
PMID: 28759640
DOI: 10.1371/journal.ppat.1006469

[…] mputational 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 s […]

library_books

A Framework to Simplify Combined Sampling Strategies in Rosetta

2015
PLoS One
PMCID: 4575156
PMID: 26381271
DOI: 10.1371/journal.pone.0138220

[…] d. 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 of […]

library_books

Automated antibody structure prediction using Accelrys tools: Results and best practices

2014
Proteins
PMCID: 4312887
PMID: 24833271
DOI: 10.1002/prot.24604

[…] sity, and more. In addition, homology models can be used to gain insight into and predict antibody-antigen interactions when used in combination with protein-protein docking methods, such as ZDOCK or SnugDock. The area of antibody design and engineering represents a special case to which homology modeling is particularly well suited, because in general the overall sequence and structural similarit […]


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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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