Swiss-PdbViewer statistics

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Number of citations per year for the bioinformatics software tool Swiss-PdbViewer
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Protocols

Swiss-PdbViewer specifications

Information


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

Versioning


No version available

Maintainer


  • person_outline Nicolas Guex

Publication for Swiss-PdbViewer

Swiss-PdbViewer citations

 (763)
library_books

A new insight into identification of in silico analysis of natural compounds targeting GPR120

2018
PMCID: 5951878
PMID: 29780684
DOI: 10.1007/s13721-018-0166-0

[…] applying spatial restraints. A bundle of 100 models from the random generation of the starting structure was calculated and subsequently the best model (with the low RMS value of superposition using Swiss-pdb viewer) (Guex and Peitsch ). To gain a better relaxation and much apart arrangement of the atoms, refinement was done on the built GPR120 model by energy minimization (EM). The stabilization […]

library_books

First comprehensive analysis of lysine acetylation in Alvinocaris longirostris from the deep sea hydrothermal vents

2018
BMC Genomics
PMCID: 5946511
PMID: 29747590
DOI: 10.1186/s12864-018-4745-3

[…] res of the two proteins were predicted by NetSurfP []. The presumed tertiary structure was established using SWISS-MODEL prediction algorithm (http://swissmodel.expasy.org/) and displayed by DeepView/Swiss-Pdb Viewer version 4.0.2. The two hemocyanin sequences were aligned with those downloaded from GenBank of other caridea shrimps using MEGA version 6.0 []. Phylogenetic trees were constructed usi […]

library_books

Isolation and molecular characterization of novel glucarpidases: Enzymes to improve the antibody directed enzyme pro drug therapy for cancer treatment

2018
PLoS One
PMCID: 5919439
PMID: 29698433
DOI: 10.1371/journal.pone.0196254

[…] Homology modeling was performed using SWISS-MODEL, a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer) []. Briefly, we searched for templates matching our target Azo CPG2 sequence. The closest enzyme, carboxypeptidase G2 (PDB ID 1CG2) with a sequence homology of 94% was used to build […]

library_books

GSTM3 and GSTP1: novel players driving tumor progression in cervical cancer

2018
Oncotarget
PMCID: 5955133
PMID: 29774096
DOI: 10.18632/oncotarget.24796

[…] ation about GSTM3 and GSTP1 []. The structural superposition of GSTP1 and GSTM3 was performed with MAMMOTH (https://ub.cbm.uam.es/software/online/mamothmult.php) and was validated and visualized with Swiss PDB viewer software (DeepView) v4.1 []. We obtained the GSTP1 model docked with the HPV16 E7 CR3 dimer model from the Mileo group [], and the GSTM3 model was obtained from the PDB database. We g […]

call_split

The IL 33 PIN1 IRAK M axis is critical for type 2 immunity in IL 33 induced allergic airway inflammation

2018
Nat Commun
PMCID: 5913134
PMID: 29686383
DOI: 10.1038/s41467-018-03886-6
call_split See protocol

[…] for modeling to provide insight regarding interaction interfaces. The resulting homology model was energy minimized, and then aligned with IRAK-2 subunits in the Myddosome structure (3mop.pdb) using DeepView. […]

library_books

Substrate Specificity of Cysteine Proteases Beyond the S2 Pocket: Mutagenesis and Molecular Dynamics Investigation of Fasciola hepatica Cathepsins L

2018
Front Mol Biosci
PMCID: 5917446
PMID: 29725596
DOI: 10.3389/fmolb.2018.00040

[…] nerated with SwissModel (Arnold et al., ) using as the principal template the crystal structure of the pro-cathepsin FhCL1 (PDB ID: 2O6X). Template and models were superimposed for visualization with Swiss PDBViewer version 4.1. (Guex and Peitsch, ; http://www.expasy.org/spdbv/). Active site residues were identified based on the literature and confirmed by structural alignment with human cathepsin […]


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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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