SymD statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SymD
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Tool usage distribution map

This map represents all the scientific publications referring to SymD per scientific context
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Associated diseases

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Popular tool citations

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Protocols

SymD specifications

Information


Unique identifier OMICS_06828
Name SymD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Information


Unique identifier OMICS_06828
Name SymD
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publications for SymD

SymD citations

 (5)
call_split

Crystal Structure of the Carboxy Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34

2017
Viruses
PMCID: 5537660
PMID: 28665339
DOI: 10.3390/v9070168
call_split See protocol

[…] risons were done with Dali [], oligomerization parameters (accessible and buried surfaces, estimated dissociation energies) were analyzed with Jspisa [] and local three-fold axes were identified with Symd []. Multiple amino acid sequences were aligned by Clustal W []. […]

call_split

Parallel SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains

2016
Biomed Res Int
PMCID: 5056246
PMID: 27747230
DOI: 10.1155/2016/4628592
call_split See protocol

[…] The SymD [] algorithm works by performing the alignment scan between the original structure and copies of itself, circularly permuted by all possible numbers of residues. It finds the score that determine […]

library_books

The bacterial dicarboxylate transporter, VcINDY, uses a two domain elevator type mechanism

2016
PMCID: 5215794
PMID: 26828963
DOI: 10.1038/nsmb.3166

[…] a TM-score of 0.52, which increased to 0.78 and 0.83 when comparing only the transport and scaffold domain helices, respectively. The analysis of the symmetry axis of the repeats was performed using SymD. . An initial sequence alignment of the template and the model sequences was compiled from the TM-align output. This initial alignment was refined by removing gaps within secondary structural ele […]

library_books

Tandem Repeats in Proteins: Prediction Algorithms and Biological Role

2015
Front Bioeng Biotechnol
PMCID: 4585158
PMID: 26442257
DOI: 10.3389/fbioe.2015.00143

[…] s.As in the case of sequence-based methods, very few comparative studies among the proposed structure-based tools have been done. In Kim et al. (), six methods (DAVROS, OPAAS, Swelfe, RQA, Gplus, and SymD) are compared in their ability to identify characteristic symmetries in fold families from CATH, SCOP, and ASTRAL databases, with SymD having an overall better performance. In Sabarinathan et al. […]

library_books

Repeat swap homology modeling of secondary active transporters: updated protocol and prediction of elevator type mechanisms

2015
Front Pharmacol
PMCID: 4560100
PMID: 26388773
DOI: 10.3389/fphar.2015.00183

[…] the domains can stymie even the most sensitive structure alignment programs. Thus, the repeats may be identified in a number of, essentially manual, ways. Two tools are available to aid this process: SymD () and CE-symm (), which take as input a single protein structure file in Protein Data Bank (PDB) format, and then report internal pseudo-symmetry within the structure (Figure ). Progressively di […]


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SymD institution(s)
Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Office of Information Technology, National Cancer Institute, National Institutes of Health, Chinakville, MD, USA

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