MEMSAT-SVM statistics

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MEMSAT-SVM specifications

Information


Unique identifier OMICS_07204
Name MEMSAT-SVM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Timothy Nugent <>

Publications for MEMSAT-SVM

MEMSAT-SVM in pipelines

 (2)
2009
PMCID: 2700806
PMID: 19470175
DOI: 10.1186/1471-2105-10-159

[…] helix svm., table shows the overall topology prediction accuracy when applying the method to the test set of 131 tm proteins, alongside results for a number of other recent topology predictors. memsat-svm and memsat3 results are fully cross-validated as described above, with all proteins homologous to the target being removed from training sets, while results for the remaining methods […]

2009
PMCID: 2700806
PMID: 19470175
DOI: 10.1186/1471-2105-10-159

[…] were extracted and psi-blast profiles were generated using the swiss-prot database. the tm/globular predictor was used to identify tm proteins, which were then subject to full topology prediction., memsat-svm is available as downloadable source code and as a web server from the url below and is free for non-commercial use. all data sets are also available, and cross-validation svm model files […]


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MEMSAT-SVM in publications

 (30)
PMCID: 5852022
PMID: 29540682
DOI: 10.1038/s41467-018-03477-5

[…] to model the invert-state based on this sequence alignment. the topological orientation of baca within the bacterial cytoplasmic membrane was predicted using sequence-based approaches topcons and memsat-svm and the structure-based method memembed., gromacs v5.1.2 was used to perform all molecular dynamics simulations (mds). coarse grained (cg) mds with the martini 2.2 force field, were used […]

PMCID: 5683752
PMID: 29159233
DOI: 10.1016/j.dib.2017.10.045

[…] (eu503126.1) with 97.2% sequence identity. the gpcrpred server predicts that this receptor belongs to the class a, rhodopsin superfamily, of g-protein coupled receptors.fig. 1fig. 1, shows the memsat-svm and memsat3 analysis of the primary sequence data of dappu-rpchr. seven transmembrane helices are predicted with a short n-terminus and long c-terminus. helix 1 runs from residue 4–22; […]

PMCID: 5578988
PMID: 28860650
DOI: 10.1038/s41598-017-10687-2

[…] fig. ). for this reason, the ab initio prediction of the helix dimer structure was crucial in the modelling process., the location of the tm segments was identified using the predictors memsat-svm, octopus and tmpred (supplementary table ). ab initio modelling of the tm segments was performed using the preddimer server, and the best model was selected according to the proposed […]

PMCID: 5462932
PMID: 28642761
DOI: 10.3389/fpls.2017.00865

[…] chosen for the present study due to its close similarity to the s. bicolor mate sequence., in addition, bdmate and sbmate transmembrane domains analysis was performed, using the softwares ffpred and memsat-svm (; ). the results are shown in the figure , where it was demonstrated that the b. distachyon mate possesses the same 12 transmembrane domains presented by the s. bicolor mate protein. […]

PMCID: 5331024
PMID: 28247289
DOI: 10.1186/s13568-017-0350-0

[…] (claros and von heijne ) was used for hydrophobicity analysis of the examined lpp-ompa-pe and non-ompa-pe amino acid sequences. structure of non-ompa-pe was predicted by tmrpres2d. memsat3 and memsat-svm was used for membrane helix prediction (nugent and jones ; nugent et al. ; http://bioinf.cs.ucl.ac.uk/psipred)., the lpp-ompa fusion gene was digested from plasmid pgem-jr with ndei […]


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MEMSAT-SVM institution(s)
Bioinformatics Group, Department of Computer Science, University College London, Gower Street, London, UK

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