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Authors Jürgen Sühnel (1993...)
(juergen.suehnel@leibniz-fli.de)
Andreas Jabs (1998 - 2000)
Jan Reichert (1998 - 2004)
Rolf Huehne (2005 - ...)
(rolf.huehne@leibniz-fli.de)
Frank-Thomas Koch (2005 - 2008)
Contact

Biocomputing Group
Institute of Molecular Biotechnology (IMB)

since October 2005

Leibniz Institute for Age Research - Fritz Lipmann Institute

since October 2015

Leibniz Institute on Aging - Fritz Lipmann Institute

Beutenbergstr.11
D-07745 Jena / Germany
+49-3641-656200
+49-3641-656210 (fax)
juergen.suehnel@leibniz-fli.de
Further contributors

Oliver Ohlenschläger
Molecular Biophysics - NMR Spectroscopy, IMB Jena
Structure determination by NMR spectroscopy

Manfred S. Weiss
Structural Biology & Crystallography, IMB Jena
Structure determination by X-ray crystallography

Thierry Moreau
Laboratory of Enzymology and Protein Chemistry, 
University François Rabelais, TOURS.
Curator of the PROLYSIS web server.
Images and annotations for the PDB entries: 1stf,1tlp,1ast,1huc,5hvp,1cew,1ice,2ptc, 3ptn,9api, 9pap.

Kristina Mehliß
Manual image generation

Peter Slickers 
Biocomputing, IMB Jena
Nucleic acid double helix and bending analysis

Christoph Schneider
Biocomputing, IMB Jena
Nucleic acid nomenclature and structure

Jesus M. Castagnetto,
Metalloprotein Database at The Scripps Research Institute
Listings of metal-containing PDB entries were generated using scripts provided by the Metalloprotein Database
[example: Sodium (Na) containing enties]

Enrico Bucci
temporarily in the IMB Jena Molecular Biophysics - NMR Spectroscopy Department
The Circular Dichroism Site

Views of biological macromolecules were generated adopting the following programs:

History and News

February 2013. The JenaLib site is moved to it's separate domain jenalib.leibniz-fli.de; all requests to the JenaLib using "www.imb-jena.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.




April 2006. The JenaLib offers a new QuickSearch Option for PDB, NDB and UniProt codes as well as for other search strings. Due to an automatic recognition mechanism only one input field is required. Thus far, information on biological units is exclusively taken from the PDB. The atlas pages offer, however, a link to the PQS Protein Structure Quaternary Server at the EBI. New color schemes are now available for coloring according to asymmetric units and chains. Coloring by Chain(Asym. Unit) assigns equal colors to symmetry-related chains, whereas Chain(Biol. Unit) colors each chain with a different color. Coloring by Asymmetric Unit assigns a specific color to each asymmetric unit that may consist of one or more chains. Finally, mapping of PROSITE patterns and SNPs is now also available for biological units. The PDB offers for NMR structures both the original PDB file and a file with so-called 'biological unit coordinates'. As compared to the original PDB file the latter file usually contains the very same structural data, but has a shortened header, occasionally renamed chain identifiers and possibly also corrections. Information from both file types is available on the atlas pages and in the Jmol viewer. Because we believe that the term 'biological unit' is misleading we have designated this second NMR structure file type by an asterisk. The thumbnail images on the atlas pages show for proteins asymmetric units and for nucleic acid-containg structures biological units. On the atlas pages information on both asymmetric and biological units is now provided. Also, in the JenaLib Jmol viewer asymmetric and biological units can be visualized on an equal footing. So, one can, for example, color complete biological units according to SCOP domains.

February 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 Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI): www.leibniz-fli.de. 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 with 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 (Jmol- jmol.sourceforge.net; thanks to Miguel Howard and to the other Jmol developers)
  • PDB/UniProt sequences and alignments that clearly indicate gaps, mutations, numbering irregularities and modified residues.

The JenaLib start page is accessible both via the old and new addresses jenalib.leibniz-fli.de/IMAGE.html and jenalib.leibniz-fli.de/IMAGE.html. The atlas pages also have two alternate URLs. Examples are:

March 2004. The atlas pages offer the Jmol Java viewer for structure rendering.

October 2003. On the atlas pages of the Image Library SCOP information is now directly displayed. A SCOP domain viewer allows for easy exploration of the (domain) structure of proteins. Note, also nucleic acids, ligands, and active-site residues are displayed. The Search Page is extended by a SCOP division.

March 2003. The IMB Jena Image Library of Biological Macromolecules features 50 Years of DNA Double Helix Structure with a poster (PDF, 600 kbytes).

December 2002. The IMB Jena Image Library offers a new Gene Ontology Interface to the PDB (GO2PDB). 

June 2002. The Search Options are substantially extended and include now SWISS-PROT gene names, SMART domain names and Pfam family names.

April 2002. The IMB Jena Image Library offers a new Genus/Species Classification Scheme.

July 2001. For all protein-containing entries a new search option via the SWISS-PROT entry name/accession number is included. This option is available on all atlas pages and on the special search page http://jenalib.leibniz-fli.de/IMAGE_PDB_SEARCH.html. The search for the SWISS-PROT entry name/accession number allows for partial string matching. This enables one to find easily all entries sharing either the first part (protein) or the second part (genus/species) of the SWISS-PROT entry name.

On http://jenalib.leibniz-fli.de/ImgLibPDB/pages/SWP/index.php tables of all PDB/SWISS-PROT cross references listed by

  • PDB code or
  • SWISS-PROT entry name or
  • SWISS-PROT protein name or
  • SWISS-PROT entry genus/species description

can be obtained.

May 2001. For human proteins links to OMIM(TM), Online Mendelian Inheritance in Man, are included.

May 2001. The Image Libray now includes links to InterPro.

May 2001. The Image Library offers a new SWISS-PROT/PDB cross-referencing scheme which is more comprehensive than the schemes implemented either in the PDB files or in SWISS-PROT. On each protein atlas page all other PDB entries containing protein chains with the same SWISS-PROT codes are listed.

April 2001. The atlas pages now include a Keyword Search tool for the web (using the Google search engine) and for PubMed.

March 2001. The Circular Dichroism Site maintained by Enrico Bucci is now hosted by the IMB Jena Image Library.

October 2000. A new environment option of the Hetero Components Database allows the systematic analysis of hetero component neighbours. A new visualization tool highlights hetero components and the corresponding environment.

May 2000. The Site Database is released. 

April 2000. Links to the OCA database and the LPC/CSU tools at the Weizmann Institute of Science are included. 

March 2000. The IMB Jena Image Library of Biological Macromolecules offers a tool for the visualization and analysis of own molecular structure files in PDB format with the standard tools used in the Image Library: RasMol/Chime, MolScript, Webmol, PDB3D (http://jenalib.leibniz-fli.de/cgi-bin/myPDB.pl)

January 2000. A compilation of the very first biopolymer structures deposited at the Protein Data Bank listed by molecule type, method of structure determination and deposition date provides information on the early days of structural biology. 

January 2000. A comprehensive bending classification of nucleic acid duples structures offers quantitative geometrical information on bending properties of nucleic acid double helix structures adopting a uniform analysis approach. 

November 1999. The Hetero Components Database is supplemented by the Periodic Table Hetero Components Element Browser. Selecting an element from the Periodic Table generates a listing of all PDB/NDB entries with this particular element included in a hetero component. 

November 1999. The Hetero Components Database now takes into account both PDB and NDB entries. 

July 1999. The Hetero Components Database is released. 

June 1999: For all metal containing PDB entries links to the Metalloprotein Database are included. In addition, compilations with metal containg entries listed by metal were generated in collaboration with the Metalloprotein Database at the Scripps Reserach Institute. These compilations can be accessed via th Periodic Table of Elements. 

May 1999: For all entries links to WHAT_CHECK are available. 

March 1999: The Base Pair Directory is included. 

January 1999: The cis-peptide division is substantially extended by including non-proline cis-peptide bonds. 

January 1999: The first parts of a contribution on experimental determination of biopolymer structures by means of X-ray crystallography are released, 

January 1999: All cis-peptide bonds,  ligands, metal ions, modified residues, and active sites can be displayed separately via RasMol/Chime/VRML-2.0 interfaces. 

December 1998:  A division on secondary structure determination of proteins by means of  FTIR spectroscopy is released. 

December 1998: A new tool for the helix and bending analysis of nucleic acid double helix structures is included. 

September 1998:  A division on proline cis-peptide bonds in proteins is included. 

August 1998:  The first part on experimental determination of biopolymer structures by means of NMR spectroscopy is released. 

July 1998:  For the automatic generation of mono and stereo vector graphics (PDF format) and VRML-2.0 scenes MolScript is used. 

June 1998: The Amino Acid Repository is released. 

May 1998: Processing is now done by means of both automatic and manual approaches. In this way all currently known 3D biopolymer structures can be accessed. In addition, RasMol, Chime and WebMol interfaces are included. 

November 1997: A three-year grant for the further development of the Image Library is acquired. 

May 1995: The first VRML representations are included. This is one of the first VRML applications in biology. 

December 1993: The IMB Jena Image Library of Biological Macromolecules was first set up as a gopher-based image archive with manually generated images for a few biopolymer structures.

Papers
J. Sühnel 
Image Library of Biological Macromolecules
Comput. Appl. Biosci. 1996, 12, 227-229 (preprint version in HTML format) (PubMed link)
J. Sühnel 
Virtual Reality Modeling for Structural Biology
In: Bioinformatics. Proceedings of the German Conference on Bioinformatics, GCB '96. Lecture notes in computer science Vol. 1278, (R. Hofestädt, T. Lengauer, M. Löffler, D. Schomburg, eds.) Springer-Verlag Berlin, 1997, 189-198 (preprint version in PDF format)
J. Sühnel 
Views of RNA on the World Wide Web
Trends in Genetics, 1997, 12, 206-207 (preprint version in PDF format) (PubMed link)
J. Reichert, A. Jabs, J. Sühnel
Virtual Reality Modeling 
Nachrichten aus Chemie, Technik und Laboratorium 1998, 46, A64-A68 (in German) (preprint version in PDF format)
J. Reichert, A. Jabs, J. Sühnel
Views of Biological Macromolecules on the World-Wide Web: The IMB Jena Image Library
Proceedings of the Workshop "Multi-Media-Systeme für Wissenschaft und Technik", 22. September 1998, Magdeburg, H.-J, Appelrath, D. Boles, K. Meyer-Wegener (Hrsg.), 141-149
(preprint version in PDF format)
J. Reichert, A. Jabs, P. Slickers, J. Sühnel
The IMB Jena Image Library of Biological Macromolecules
Nucleic Acids Res. 2000, 28, 246-249 (preprint version in PDF format) (PubMed link)) (journal link))
J. Reichert, J. Sühnel
The IMB Jena Image Library of Biological Macromolecules: 2002 update
Nucleic Acids Res. 2002, 30, 253-254 (preprint version in PDF format) (PubMed link) (journal link)
Databases that offer links to the Image Library
Reviews, Responses, Presentations
  • The Image Library of Biological Macromolecules has been featured as website of the day on February 20, 1997 by the 'webzine' HMS Beagle. (PDF ) 
  • It has been chosen as a selection for the Scout report on September 5, 1997. 
  • WebWatch - Cool Images (Science 1997, 278, 1089) (PDF) 
  • Information from the IMB Jena Image Libray has been used by ScienceFriday on
    • October 23, 1998: Protein Folding with P. Kollman, L. Regan, F. Cohen (PDF)
    • November 13, 1998: Legal and Ethical Issues of DNA Science with P. Ossorio, N. Elster, E. Pergament (PDF)
    • March 12, 1999: Biotech History/Biotech Future with D. Koshland, E. Penhoet, P. Rabinow (PDF)
  • NetWatch - Site Visit (Science 1999, 283, 755) (GIF | PDF ) 
  • This website has been chosen as a four-star "indispensible" site in the BioMedLink database. 
  • The Image Library has been investigated by BioWeb, an online life sciences magazine in June 1999 ( PDF ). 
  • The Image Library has been included in the Encyclopedia Britannica as a two-star site (search topic: macromolecule) and has received the  (January 2000). 
  • The Institute for Scientific Information (ISI) has included the Image Library in  , a collection of evaluated websites (March 2000). 
  • The Image Library has been mentioned in the Adress Book section of BIONEWS (Vol 13, 05/2000) (PDF).
  • Images from the IMB Jena Image Library have been featured in the Feuilleton of the Frankfurter Allgemeine Zeitung (FAZ) on November 21, 2000 in an article entitled: Zehn Ansichten zur Architektur des Lebens.  The structures shown are the integration host factor and rhodopsin.See the article and a negated image . 
  • The IMB Jena Image Library of Biological Macromolecules has been included in the World Index of Molecular Visualization Resources (November 2000). 
  • In an article entitled Die Mär vom Leben ohne Krankheit the Süddeutsche Zeitung has shown a large image of the nucleosome core particle on December 30, 2000. See a low-resolutionand a high-resolution image. The Hamburger Abendblatt features in the article Faszination des Lebendigen on January 2, 2001 many structure images from the Image Library. See the article in high quality (92 Mbytes) and low quality (224 Kbytes). 
  • Science has featured the Image Library as Site of the Month in April 2001 (PDF). 
  • The IMB Jena Image Library has received the Top Chemical Content Site Award of chemie.de in April 2001 (PDF).
  • See a poster on the Image Library that will be shown in the shopping mall Goethe-Galerie between November 2 and 4, 2001 (in German).
  • The IMB Jena Image Library has been selected by the U.S. National Science Teacher's Association (NSTA) for inclusion in SciLinks (October 2002).
  • The journal RNA uses images from the Jena Library of Biological Macromolecules - JenaLib as cover images for all 2003/2004/2005/2006/2007 issues.
  • The Neue Züricher Zeitung am Sonntag features images of ideal A-DNA, B-DNA and Z-DNA from the Image Library in an article by Ernst Peter Fischer entitled "Die zweite Entdeckung" (April 20, 2003).
Books that use images from the Image Library
Exhibits that have used images or animations of the Image Library
  • Gen-Welten. Werkstatt Mensch (1 | 2)?, March 27, 1998 - January 10, 1999 (Deutsches Hygiene-Museum, Dresden / Germany)  
  • ZOOM IN.OUT (1 | 2 | 3), March 23-29, 1998 (laboratorio dell' immaginario scientifico, Trieste / Italy)  
Copyright
Please contact the database authors for further information.
Funding
Between January 1998 and February 2001 the Image Library has been supported by the.
Since 1995 the database is funded by
Last update: February 13, 2006 Image Library Home | JenaLib Home