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SymmDock specifications

Information


Unique identifier OMICS_23430
Name SymmDock
Interface Web user interface
Restrictions to use None
Input data One molecule and the symmetry order.
Output data A list of candidate complexes between user specified receptor and ligand molecule.
Computer skills Basic
Version 1.0
Stability Beta
Maintained Yes

Maintainers


  • person_outline Haim Wolfson
  • person_outline Dina Schneidman-Duhovny

Additional information


http://bioinfo3d.cs.tau.ac.il/SymmDock/symmdock.html

Information


Unique identifier OMICS_23430
Name SymmDock
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data One molecule and the symmetry order.
Output data A list of candidate complexes between user specified receptor and ligand molecule.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Haim Wolfson
  • person_outline Dina Schneidman-Duhovny

Additional information


http://bioinfo3d.cs.tau.ac.il/SymmDock/symmdock.html

Publications for SymmDock

SymmDock citations

 (26)
library_books

Type IX secretion system PorM and gliding machinery GldM form arches spanning the periplasmic space

2018
Nat Commun
PMCID: 5790014
PMID: 29382829
DOI: 10.1038/s41467-017-02784-7

[…] larger than 1.4 mda of the (porklmn)2 complex and from vincent et al., together with the structures reported here, we speculated on the possible architecture of the t9ss core machinery. we used symmdock software to identify which part of porm/gldm might fit together to form a multimer of dimers. using the straight gldmp structure, both threefold and fourfold symmetry created associations […]

library_books

Structure analysis of capsid protein of Porcine circovirus type 2 from pigs with systemic disease

2017
PMCID: 5914143
PMID: 29128395
DOI: 10.1016/j.bjm.2017.08.007

[…] validated and used to build the capsid structure. stereochemical quality and accuracy of the predicted model were evaluated using ramachandran plot analysis., the pentamer was generated by symmdock server and the generated models were visualized and compared to pcv2cs capsid protein using the pymol version 1.3 (schrodinger, llc). additionally, the model was submitted to the structure […]

library_books

Unraveling the Self Assembly of the Pseudomonas aeruginosa XcpQ Secretin Periplasmic Domain Provides New Molecular Insights into Type II Secretion System Secreton Architecture and Dynamics

2017
MBio
PMCID: 5646246
PMID: 29042493
DOI: 10.1128/mBio.01185-17

[…] in the hexamerization of xcpqn012 dimers., our in vitro data revealed that xcpqn012 oligomerizes into a hexamer of dimers. in order to improve our understanding of xcpq multimerization, we used the symmdock server (, ) to generate a dodecameric complex assuming c6 symmetry by imposing the xcpqn012 dimer as an asymmetric subunit. we kept the best model based on symmdock criteria and tested […]

library_books

Methods used to study the oligomeric structure of G protein coupled receptors

2017
Biosci Rep
PMCID: 5398257
PMID: 28062602
DOI: 10.1042/BSR20160547

[…] which can then be either used to design experiments to test the possible dimer configurations []., among all the docking programs tested by kaczor et al. [] (zdock, cluspro, hex, gramm-x, patchdock, symmdock, haddock, 3d-garden and rosetta), gramm-x performs optimally in modelling tm complexes []. this program was used to model the 5-ht4 receptor homodimer, which identified tm2/4 and tm4/6 […]

library_books

Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies

2017
Sci Rep
PMCID: 5427971
PMID: 28331186
DOI: 10.1038/s41598-017-00266-w

[…] assemblies for which the multimeric conformation is already known, and compared the results with previously proposed methods including a particle swarm optimization (pso) pow er , multifit and symmdock (see methods and supplementary table ). for each of the assembly cases, em maps at 15 å resolution were synthetically generated and used to rank the best candidate solutions. ranking […]

library_books

Nucleoplasmin like domain of FKBP39 from Drosophila melanogaster forms a tetramer with partly disordered tentacle like C terminal segments

2017
Sci Rep
PMCID: 5225439
PMID: 28074868
DOI: 10.1038/srep40405

[…] fkbp39 molecules, we cannot ignore the possibility of an alternative oligomerization state. to develop reliable models of fkbp39 in solution, the tetramer of the npl domain was generated using the symmdock server and the nmr structure of the isolated n-terminal domain of d. melanogaster fkbp39 (pdb id: 4ca9). the atomic model of the c-terminal fkbd (residues 196–353) was downloaded […]


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SymmDock institution(s)
School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel; Sackler Institute of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Basic Research Program, SAIC-Frederick Inc., Laboratory of Experimental and Computational Biology NCI-Frederick, Frederick, MD, USA
SymmDock funding source(s)
Supported in part by the Center of Excellence in Geometric Computing and its Applications funded by the Israel Science Foundation (administered by the Israel Academy of Sciences); by the Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University; by the Eshkol Fellowship funded by the Israeli Ministry of Science; by Federal funds from the National Cancer Institute, National Institutes of Health, under contract number NO1-CO-12400.

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