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CSB specifications

Information


Unique identifier OMICS_09827
Name CSB
Alternative name Computational Structural Biology Toolbox
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Ivan Kalev

Publication for Computational Structural Biology Toolbox

CSB citations

 (4)
library_books

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle

2016
Sci Rep
PMCID: 5120318
PMID: 27876851
DOI: 10.1038/srep37536

[…] ti) were assigned to OrthoMCL orthologous groups, and the presence or absence of groups was compared among the different species using ad hoc scripts from scriptome (http://archive.sysbio.harvard.edu/csb/resources/computational/scriptome/UNIX/). […]

library_books

Confidence Guided Local Structure Prediction with HHfrag

2013
PLoS One
PMCID: 3797814
PMID: 24146881
DOI: 10.1371/journal.pone.0076512

[…] The fragment filtering algorithm and the confidence-guided torsion angle predictor are implemented as an HHfrag extension in version 1.2 of the CSB open-source SDK . An HHfrag web server is available at http://toolkit.tuebingen.mpg.de/hhfrag. The standalone executable, source code and Python API are freely available for download at http://csb […]

library_books

β Propeller Blades as Ancestral Peptides in Protein Evolution

2013
PLoS One
PMCID: 3797127
PMID: 24143202
DOI: 10.1371/journal.pone.0077074

[…] ode to obtain an all-vs-all matrix of similarity p-values. These p-values were extracted from the result files and converted to a CLANS input file using the bio.io.hhpred and bio.io.clans modules of CSB, respectively . The cluster map was computed from the input file using the force-directed layouting method implemented in CLANS (attract and repulse value 10) at a p-value threshold of 1e-5 until […]

library_books

Description and Nomenclature of Neisseria meningitidis Capsule Locus

2013
PMCID: 3647402
PMID: 23628376
DOI: 10.3201/eid1904.111799

[…] t is necessary to have nomenclature that identifies the serogroup simply and quickly. The polysialyltransferase genes belonging to serogroups B and C share >70% sequence identity and should be termed csb and csc, respectively. The equivalent gene in serogroups W and Y is also a sialyltransferase, but it also has a glycosyltransferase function and is distinct from the serogroups B and C genes. Thes […]

Citations

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CSB institution(s)
Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
CSB funding source(s)
Contract research ‘Methoden in den Lebenswissenschaften’ of the Baden-Württemberg Stiftung, by Deutsche Forschungsgemeinschaft (DFG) grant HA 5918/1-1 and by the Max Planck Society

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