Swiss-PdbViewer protocols

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Swiss-PdbViewer specifications

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Unique identifier OMICS_05043
Name Swiss-PdbViewer
Alternative names DeepView, Swiss-Pdb Viewer
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 Nicolas Guex <>

Publication for Swiss-PdbViewer

Swiss-PdbViewer in pipelines

 (12)
2018
PMCID: 5785021
PMID: 29370294
DOI: 10.1371/journal.ppat.1006840

[…] three-dimensional structure of e. festucae small gtpases were predicted by iterative threading assembly refinement (i-tasser) [] with the template library updated on 17 mar 2017, and drawn using swiss-pdbviewer []., the deduced protein sequences of fungal small gtpases () were aligned using the clustalw program [] with default settings. phylogenetic analysis was conducted using […]

2018
PMCID: 5890266
PMID: 29632392
DOI: 10.1038/s41598-018-23997-w

[…] model was chosen to analyze contacts between ehcfim25 residues and the guug molecule by the cma (contact map analysis) software (http://ligin.weizmann.ac.il/cma/). for some analyses, we used the swiss-pdbviewer 4.10 software (http://www.expasy.org/spdbv/) to obtain the mutant ehcfim25*l135t protein., md simulations of ehcfim25 protein alone or interacting with the guug motif were performed […]

2016
PMCID: 4809597
PMID: 27019095
DOI: 10.1371/journal.pone.0152251

[…] were placed in the 3-dimensional structure model of poliovirus capsid protomer, based on x-ray crystallographic analysis of type 2 poliovirus strain lansing (pdb id: 1eah) [] using the software swiss-pdbviewer []. the genbank accession number of isolate 44624 complete genome sequence is ku372652., the time interval between the date of opv administration and the data of sampling of the vdpv2 […]

2016
PMCID: 4941113
PMID: 27387148
DOI: 10.1038/ncomms12138

[…] default parameters. the model quality was evaluated using the structure assessment tools of the swiss-model workspace, including anolea, dfire and qmean. structures were viewed using the deepview/swiss-pdbviewer 4.1 (http://www.expasy.org/spdbv/). multiple sequence alignments of hma proteins were conducted in bioedit software using the clustalw method., the seeds of usda rice core collection […]

2016
PMCID: 4943180
DOI: 10.1093/gbe/evw108

[…] is a combination of template modelling and ab initio folding simulation). the predicted model and relevant amino acids from our functional divergence and positive selection analyses were viewed in swiss-pdbviewer version 4.1 ()., we used the program mafft to generate the multiple sequence alignments (msa). all maximum likelihood (ml) phylogenetic trees were obtained with raxml v.7.2.8 software […]


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Swiss-PdbViewer in publications

 (325)
PMCID: 5905236
PMID: 29696031
DOI: 10.3389/fpls.2018.00474

[…] modification., homology models of nr protein from eight species were constructed in the swiss-model workspace. the molecular surface and the electrostatic potential were computed with swiss-pdbviewer v.4.0.1 software (). cys residues distributed on the protein surface were further analyzed (figure ). as a previous report suggested, negative or neutral electrostatic potentials […]

PMCID: 5894206
PMID: 29636017
DOI: 10.1186/s12870-018-1274-9

[…] and structural models are in additional file : figure s3b. mkk5 and mkk7 structural predictions were performed with i-tasser [], using mek1 (1s9j) to assist the prediction. models were explored with swiss-pdbviewer v4.1 and fit with the magic fit button []. structural features were extracted from models and overlaid on the primary sequence (additional files , and : figures s3–s5)., domain swap […]

PMCID: 5890266
PMID: 29632392
DOI: 10.1038/s41598-018-23997-w

[…] model was chosen to analyze contacts between ehcfim25 residues and the guug molecule by the cma (contact map analysis) software (http://ligin.weizmann.ac.il/cma/). for some analyses, we used the swiss-pdbviewer 4.10 software (http://www.expasy.org/spdbv/) to obtain the mutant ehcfim25*l135t protein., md simulations of ehcfim25 protein alone or interacting with the guug motif were performed […]

PMCID: 5819190
PMID: 29463214
DOI: 10.1186/s12864-018-4549-5

[…] predict the theoretical pi (isoelectric point) and mw (molecular weight). the number of α-helix, β-strand and β-sheet structures, number of cavities, superficial area and volume were estimated using swiss-pdbviewer (http://www.expasy.org/spdbv/). we took into consideration that we observed differences in the number of cavities, so we included additional peptidases in the analysis. a total of 50 […]

PMCID: 5931241
PMID: 29453195
DOI: 10.1136/jmedgenet-2017-104954

[…] modelling of p.arg99his was performed using swiss-model, an automated homology modelling program (http://swissmodel.expasy.org/workspace/). data obtained by the homology models were visualised using swiss-pdbviewer 4.1. multiple sequence alignment was performed according to a homologene program., slides spanning the entire inner ear from three different mice were stained, and the observed […]


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Swiss-PdbViewer institution(s)
Geneva Biomedical Research Institute, Glaxo Wellcome Research and Development, Plan-les-Ouates/Geneva, Switzerland

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