Jena3D replaces the JenaLib Jmol Viewer within the JenaLib. Jena3D has its own homepage but is still closely linked to the JenaLib.
Jena3D also introduces a Sequence/Alignment viewer that is uncoupled from the JenaLib atlas pages.
Jena3D contains a mirror of the Jmol interactive scripting documentation.
The JenaLib atlas pages now provide an exon mapping table with direct links to the corresponding ENSEMBL and UniProtKB pages.
The JenaLib Jmol Viewer now offers an exon standard view, highlighting exons and exon boundaries. These can also be adressed and highlighted individually by specific control elements.
Briefings in Functional Genomics and Proteomics Advance Access published October 23, 2007 (doi:10.1093/bfgp/elm020)
Rolf Hühne, Frank-Thomas Koch and Jürgen Sühnel
The PDB Remediation Project is a joint effort of the members of the wwPDB (RCSB PDB, MSD-EBI, PDBj, BMRB).
It aims to provide a uniform remediated structural dataset in all three file formats (PDB, mmCIF, PDBXML) that are used to distribute the Protein Data Bank (PDB).
An overview of the project and the resulting changes is provided in this PDF document.
The SCOP and CATH domain descriptions presented in the JenaLib were adapted to the remediated PDB data (e.g.: chain identifier " " changed to "A").
It diplays either the SCOP or CATH classification hierarchy and provides control buttons to collapse/expand specific hierarchy levels at once. Each tree node can also be collapsed/expanded individually.
The atlas page of each PDB entry classified in SCOP/CATH contains the entry-specific part of the tree. By clicking on the name of any displayed hierarchy level (e.g.: GroES-like) the whole tree below this level can be explored with the Tree Browser.
At the top of the Tree Browser a SCOP or CATH search option is integrated.
Additionally the visualization of CATH domains was added to the Jenalib Jmol Viewer.
The 3508 CancerSNPs described by the authors were mapped onto PDB structures using information from the CCDS, ENSEMBL and
UniProtKB/Swiss-Prot databases. (current mapping statistics)
This allows to select PDB entry sets related to human ageing.
In addition, OMIM cross references from GenAge and UniProt are now included in the entry list customization scheme.
Entry sets can be selected according to
The user can select the desired output columns (currently from a list of 26 columns) and it is also possible to sort the output according to information indicated in any of the columns.
The output format is either HTML or ASCII (tab-separated text).
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