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SWISS-MODEL Repository specifications

Information


Unique identifier OMICS_03033
Name SWISS-MODEL Repository
Restrictions to use None
Maintained Yes

Documentation


Maintainer


  • person_outline Torsten Schwede

Publications for SWISS-MODEL Repository

SWISS-MODEL Repository citations

 (30)
library_books

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

2018
Sci Rep
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] he filtered set of secreted and cell membrane proteins in A. fumigatus Af293, and in such cases, the protein structure models from ModBase (https://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi) and SWISS-MODEL repository (https://swissmodel.expasy.org/repository) were used to evaluate structural similarity. Note that only protein structure models which have more than 40% sequence identity with t […]

call_split

Characterization of indole 3 pyruvic acid pathway mediated biosynthesis of auxin in Neurospora crassa

2018
PLoS One
PMCID: 5805262
PMID: 29420579
DOI: 10.1371/journal.pone.0192293
call_split See protocol

[…] blish the consistency and reliability of each method, as well as the structure. We used the Ab initio method from the I-TASSER (http://zhanglab.ccmb.med.umich.edu/I-TASSER/) online-server [] and the "SWISS-MODEL Repository portal" (http://www.expasy.org/) for homology modeling []. For the Ab initio method, corresponding enzyme sequences from N. crassa were submitted to the I-TASSER server, and the […]

call_split

Betanodavirus B2 protein triggers apoptosis and necroptosis in lung cancer cells that suppresses autophagy

2017
Oncotarget
PMCID: 5706861
PMID: 29212215
DOI: 10.18632/oncotarget.21588
call_split See protocol

[…] SWISS-MODEL Repository (SMR) and Phyre2 web portal are a database of annotated 3D protein structure models generated by the automated SWISS-MODEL homology modeling pipeline [, ] and Phyre2 web portal […]

library_books

An overview of comparative modelling and resources dedicated to large scale modelling of genome sequences

2017
Acta Crystallogr D Struct Biol
PMCID: 5571743
PMID: 28777078
DOI: 10.1107/S2059798317008920

[…] dels for the 12 most accessed genomes in UniProtKB. It houses more than 900 000 models for UniProt sequences. Of the 21 042 human sequences, ∼75% are annotated with at least one structural model. The SWISS-MODEL repository also provides structural models for homo-oligomeric complexes. All of the homology models were created using the in-house modelling platform PROMOD3 (Bienert et al., 2017), whic […]

library_books

Conformational plasticity and evolutionary analysis of the myotilin tandem Ig domains

2017
Sci Rep
PMCID: 5479843
PMID: 28638118
DOI: 10.1038/s41598-017-03323-6

[…] mployed molecular dynamics simulations. First, we produced models of tandem Ig domains of myotilin using I-TASSER, with the Z-score as a selection criteria. Comparatively, best model generated in the Swiss-model repository showed almost identical structure with the RMSD value of 1.16 Å between 191 equivalent Cα atoms and almost coaxial orientation. For the molecular dynamics simulations the best m […]

library_books

Nucleoplasmin like domain of FKBP39 from Drosophila melanogaster forms a tetramer with partly disordered tentacle like C terminal segments

2017
Sci Rep
PMCID: 5225439
PMID: 28074868
DOI: 10.1038/srep40405

[…] he SymmDock server and the NMR structure of the isolated N-terminal domain of D. melanogaster FKBP39 (pdb id: 4CA9). The atomic model of the C-terminal FKBD (residues 196–353) was downloaded from the SWISS-MODEL Repository. This structure was modelled on the basis of the FKBD domain structure of the Fpr4 protein (51.33% identity, PDB id: 4BF8), which also possesses an N-terminal NPL domain and a C […]

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SWISS-MODEL Repository institution(s)
Biozentrum, University of Basel, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Basel, Switzerland
SWISS-MODEL Repository funding source(s)
Supported by SIB Swiss Institute of Bioinformatics; Swiss Foundation for Excellence and Talent in Biomedical Research.

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