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Protocols

SDM specifications

Information


Unique identifier OMICS_07148
Name SDM
Alternative name Site Directed Mutator
Interface Application programming interface
Restrictions to use None
Input data A PDB file or a PDB code and the point mutation specified as a string containing the single letter code of the wildtype residue in the protein.
Input format PDB
Output format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Tom Blundell
  • person_outline Arun Prasad Pandurangan

Publications for Site Directed Mutator

SDM citations

 (22)
library_books

The first case of NSHL by direct impression on EYA1 gene and identification of one novel mutation in MYO7A in the Iranian families

2018
PMCID: 5817178
PMID: 29511501
DOI: 10.22038/IJBMS.2018.26269.6441

[…] erformed. Afterward, the complete project file was submitted to SWISS-MODEL. The effects of amino acid substitution on MYO7A were analyzed and predicted by in-silico tools such as I-mutant 2.0 () and site-directed mutator instruments (SDM) (). The whole protein aggre-gation propensities in its folded states were predicted by Aggrescan3D (). In order to verify the obtained 3D structure, ProSA (http […]

library_books

BEST1 protein stability and degradation pathways differ between autosomal dominant Best disease and autosomal recessive bestrophinopathy accounting for the distinct retinal phenotypes

2018
Hum Mol Genet
PMCID: 5905664
PMID: 29668979
DOI: 10.1093/hmg/ddy070

[…] nalysis we relied on the recently solved 3D protein structure of chicken BEST1 (cBESTcryst) (), which was implemented into the structure-based prediction tools mutation cutoff scanning matrix (mCSM), site-directed mutator (SDM), DUET and the three-state predictor I-mutant 2.0. Accordingly, the analyzed pathologic mutations were all classified as destabilizing noticeable by a large decline in Gibbs […]

library_books

Vermont: a multi perspective visual interactive platform for mutational analysis

2017
BMC Bioinformatics
PMCID: 5606220
PMID: 28929973
DOI: 10.1186/s12859-017-1789-3

[…] rategies that have been proposed to understand and predict the impact of mutations on protein structure and function based on different perspectives.Worth and colleagues proposed in [] the web server Site Directed Mutator (SDM) [], which uses a statistical potential energy function to predict the effect of SNPs on the stability of proteins based on environment-specific amino acid substitution freq […]

library_books

Mycobacterium tuberculosis Glyceraldehyde 3 Phosphate Dehydrogenase (GAPDH) Functions as a Receptor for Human Lactoferrin

2017
PMCID: 5462994
PMID: 28642848
DOI: 10.3389/fcimb.2017.00245

[…] predict the effect of these alterations on protein stability and proximity to substrate binding site. The effect of mutations on protein stability were analyzed using DUET (Pires et al., ), mCSM and Site Directed Mutator (SDM) (Worth et al., ). […]

library_books

In silico analyses of deleterious missense SNPs of human apolipoprotein E3

2017
Sci Rep
PMCID: 5449402
PMID: 28559539
DOI: 10.1038/s41598-017-01737-w

[…] The following methods either combine information from protein sequence and structure or use protein structural information alone to analyze missense variants: PolyPhen, Site Directed Mutator (SDM), Fold-X and PoPMuSiC. […]

call_split

Novel compound heterozygous MYO7A mutations in Moroccan families with autosomal recessive non syndromic hearing loss

2017
PLoS One
PMCID: 5417485
PMID: 28472130
DOI: 10.1371/journal.pone.0176516
call_split See protocol

[…] visualization of the predicted structures were performed using YASARA software []. To analyse the impact of amino acid substitutions on MYO7A protein structure stability, we used MAESTROweb and SDM (Site Directed Mutator) bioinformatics tools [,]. […]

Citations

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SDM institution(s)
Department of Biochemistry, University of Cambridge, Cambridge, UK; Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC, Australia
SDM funding source(s)
Supported by Gates HIT-TB and the EU MM4TB [Project ID: 260872]; Bill & Melinda Gates Foundation [RG60453]; Jack Brockhoff Foundation [JBF 4186, 2016]; C.J. Martin Research Fellowship from the National Health and Medical Research Council of Australia [APP1072476]; Wellcome Trust Programme Grant [093167/Z/10/Z]; Newton Fund RCUK-CONFAP Grant awarded by The Medical Research Council (MRC) [MR/M026302/1].

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