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CSDB specifications

Information


Unique identifier OMICS_09238
Name CSDB
Alternative name ClustScan database
Restrictions to use None
Maintained No

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Publication for ClustScan database

CSDB citations

 (4)
library_books

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

2016
PMCID: 5640684
PMID: 29062930
DOI: 10.1016/j.synbio.2015.12.002

[…] can is a Java-based desktop application that offers mining for PKS and NRPS gene clusters in a convenient graphical user interface. ClustScan was used to compile and analyze the data contained in the ClustScan database (see below). NP.searcher is a web-based software program with an emphasis on structure prediction of the putative peptide or polyketide metabolites. NaPDoS uses BLAST and HMMer to i […]

library_books

Multilocus Sequence Analysis for Assessment of Phylogenetic Diversity and Biogeography in Thalassospira Bacteria from Diverse Marine Environments

2014
PLoS One
PMCID: 4157779
PMID: 25198177
DOI: 10.1371/journal.pone.0106353

[…] e robustness of the tree topologies. Additionally, phylogenies from distance matrix by neighbour-joining method the clustering tree based on the DDH was constructed with the web server (http://genome.csdb.cn/cgi-bin/emboss/fneighbor). […]

library_books

Tautomerism in large databases

2010
J Comput Aided Mol Des
PMCID: 2886898
PMID: 20512400
DOI: 10.1007/s10822-010-9346-4

[…] ce a much smaller number of generated tautomers can be expected. This is exactly what we found when we applied Epik to a small subset of 700 structures chosen to represent the tautomeric diversity in CSDB and compared the number of generated tautomers to the results of our approach. Such comparisons are therefore of limited relevance for the questions we tried to address in this study.The price fo […]

call_split

Structural insights into RNA dependent eukaryal and archaeal selenocysteine formation

2007
Nucleic Acids Res
PMCID: 2275076
PMID: 18158303
DOI: 10.1093/nar/gkm1122
call_split See protocol

[…] DRAWTREE in the Phylip 3.66 package (). A similar structure-based alignment was used for the structure-based sequence alignment shown in . First, SepSecS was structurally aligned to SepCysS, IscS and CsdB. This structure-based alignment was then supplemented with three additional SepSecS sequences, which had been previously aligned to MMPSepSecS with CLUSTAL (). Some alignment ambiguities were cor […]

Citations

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CSDB institution(s)
Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva, Zagreb, Croatia; Croatian Accreditation Agency, Vukovarska, Zagreb, Croatia; Institute of Pharmaceutical Science, King’s College London, London, UK; Department of Chemistry, King’s College London, London, UK; Department of Genetics, University of Kaiserslautern, Kaiserslautern, Germany

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