JenaLib Site has moved to jenalib.leibniz-fli.de - Feb 8, 2013
The JenaLib site has moved to it's separate domain jenalib.leibniz-fli.de
all requests to the JenaLib using "jenalib.leibniz-fli.de" or "www.leibniz-fli.de" should transparently get redirected to
jenalib.leibniz-fli.de. Note that all JenaLib addresses and links on this page have been converted to the new site address.
Jenalib Jmol Viewer becomes Jena3D - Nov 14, 2008
An enhanced version of the JenaLib Jmol Viewer
has been released as Jena3D
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.
Exons mapped onto PDB structures - Oct 30, 2007
Exon information from the ENSEMBL
databases is used to map exons onto PDB structures.
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.
Review on comprehensive resources on 3D biological macro-molecule structures - Oct 23, 2007
See our review:
"A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules"
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
JenaLib now based on remediated PDB files - Sep 4, 2007
The JenaLib is now based on remediated PDB file data.
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").
New SCOP/CATH 'Classification Tree Browser' - May 30, 2007
The JenaLib offers a new user-friendly SCOP
structure classification Tree Browser
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.
CancerSNPs from article 'Sj÷blom et al., Science 314, 268-274 (2006)' mapped onto PDB structures - March 16, 2007
New features 'Age Related' and 'OMIM' for customizing entry lists - December 13, 2006
The information of the GenAge
database is integrated into the 'Customize Entry List
' option of the JenaLib.
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.
New option for customizing entry lists - September 18, 2006
The JenaLib offers a new very versatile option for customizing entry lists.
Entry sets can be selected according to
- Molecule type
- Other structural features
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).
New 'QuickSearch' option and 'Biological Unit' integration - April 27, 2006
Why a new name? - February 10, 2006
The IMB Jena Image Library of Biological Macromolecules
has served the scientific and educational communities for more than 10 years (since 1993).
In October 2005 the hosting Institute of Molecular Biotechnology - IMB
has changed its name to
Therefore, we have decided to change the database name to
Jena Library of Biological Macromolecules (JenaLib).
This name change is accompanied by a number of other changes including:
- redesigned start and atlas pages (the other pages will follow soon)
- integration of data on single amino acid polymorphisms (SAPs), taken from UniProt, and PROSITE motifs
PDB, SCOP, other UniProt, Gene Ontology and NCBI taxonomy information
- a new Jmol-based molecule viewer that offers integrated viewing
of ligand, site, SAP, PROSITE and SCOP information
- PDB/UniProt sequences and alignments that clearly indicate gaps, mutations, numbering irregularities and modified residues.
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