8th Pharma Relay
8th Pharmastaffellauf will again take place at the Schlossberg: Please register your teams more information here.
NANPDB: Publication of Natural products database
SeMPI - Publication of new web server
Text mining application
New Member: Paul Zierep
We welcome Paul Zierep as new Member of the Research group.
7th Pharma Relay
7th Pharmastaffellauf took place at the Schlossberg: 5 members of a team had to run 3 km each. Please find here some photos of Pharma Relay 2016.
We had our Instituteday 2016 at Schaunsland on 4th of August. For photos please contact Kiran Telukunta.
New Member: Gwang-Jin Kim
We welcome Gwang-Jin Kim as new Member of the Research group.
New publication in NAR
We proudly present our update publication in Nucleic Acids Research: "StreptomeDB 2.0 – an extended resource of natural products produced by streptomycetes." Check it out in our publications page!
6th Pharma Relay
On the 30th of September, 2015, the 6th edition of the traditional Pharma Relay took place at Schlossberg. Enjoy the photos and time sheet Pharma Relay 2015.
Cover Issue of the J. Chem. Inf. Model.
Target fishing by cross-docking to explain polypharmacological effects
The Purchasable Chemical Space: A Detailed Picture
5th Pharma Relay
On the 16th of September, 2014, the 5th edition of the traditional Pharma Relay took place at Schlossberg. Enjoy the report: Pharma Relay 2014.
Publications in Cheminformatics
We have recently published two stories in cheminformatics --- Check them out in our publications page!
Problems dealing with small molecules? Try out our testing server of the ChemicalToolBoX! (ctb.pharmaceutical-bioinformatics.org)
New publication in epigenetics
We proudly present our new publication in epigenetics: "Targeting the BET family for the treatment of leukemia". Check it out in our publications page!
New member: Mehrosh Pervaiz
Visit the Lab Members page and meet Mehrosh.
New member: Dennis Klementz
Visit the Lab Members page and meet Dennis.
New Agent against Cancer Cells
A new active substance was discovered that inhibits cell division in leukemia cells and could play an important role in the fight against cancer (Publication).
DPhG - Annual meeting 2013
Please follow this link to see a Livestream of the short poster lectures on Wednesday, Oct. 9th at 17:45.
On the 3rd of September 2013, the fourth Pharma relay has taken place at the Schlossberg. By having sunny weather all teams have done their best ... (more infos)
New paper published
A virtual screening campaign followed by an experimental validation in inhibition of the P-glycoprotein revealed a new Pgp-inhibitor. Please find here the manuscript: PubMed
New associate member
The Research Group Pharmaceutical Bioinformatics is now an associate member of the SFB992 - Medical Epigenetics
3. Pharma Relay
Our group was proud to organize the third Pharma relay ... (more infos)
Our group was proud to organize the institute day 2012. (more infos)
Release of the ChemicalBoX!
The largest freely available comprehensive collection of chemical compounds!! CHECK IT OUT NOW through our ftp server or clone it with Git: "git clone http://chemicalbox.pharmaceutical-bioinformatics.org/chemicalbox.git"
prolific - new webserver
Prolific is a new webserver that is now accessible under
http://www.pharmazeutische-bioinformatik.de/prolific. Prolific is an extension of CIL and allows to BLAST the literature database PubMed for protein-compound interactions. The paper has been recently accepted at "Bioinformatics" PubMed.
Pharma Relay 2011
Our group was proud to organize the second Pharma relay. The 18th of October was a sunny day and 10 enthusiastic teams followed our call of joining us ... (more infos)
Streptomyces Tü6071 - genome sequence available now
We are pleased to announce the new genome sequence of Streptomyces Tü6071.
The paper has been accepted at "Journal of Bacteriology" and will be available soon.
Erxleben A, Wunsch-Palasis J, Grüning BA, Luzhetska M, Bechthold A, Günther S (2011) Genome sequence of Streptomyces sp. Tü6071. J Bact 193 (16), in press.
Streptomyces sp. Tü6071 is a soil-dwelling bacterium which has a highly-active isoprenoid biosynthesis. Isoprenoids are important precursors for biopharmaceutical molecules such as antibiotics or anti-cancer agents, e.g. Landomycin. Streptomyces sp. Tü6071 produces the industrially important terpene glycosides Phenalinolactones which have anti-bacterial activity against several Gram-positive bacteria. The availability of the genome sequence of Streptomyces sp. Tü6071 allows for understanding the biosynthesis of these pharmaceutical molecules and will facilitate rational genome modification to improve industrial use.
Pharma Relay 2011, october 18th, 4 p.m.
With the very positive feedback for the last year, we are glad to organize the 2nd Pharma Relay, taking place on tuesday, october 18th, 4 p.m., again at the "Burghaldenring, Schlossberg". All faculty members of the Institute of Pharmaceutical Sciences are invited to take part in groups of 5 persons. To register, please, send an e-mail to stephan[dot]flemming[at]pharmazie[dot]uni-freiburg[dot]de.
CIL - Compounds in Literature
We are pleased to announce our new webserver "CIL" is now accessible to public and available under
The paper has been accepted at "Bioinformatics" and will be available soon.
Summary: Searching for certain compounds in literature can be an elaborate task, with many compounds having several different synonyms. Often, only the structure is known but not its name. Furthermore, rarely-investigated compounds may not be described in the available literature at all. In such cases, preceding searches for described similar compounds facilitate literature mining. Highlighted names of proteins in selected texts may further accelerate the timeconsuming process of literary research. Compounds In Literature (CIL) provides a web interface to automatically search with names, structures, and similar structures the over 28 million compounds of PubChem and more than 18 million citations provided by the PubMed service. CIL’s pre-calculated database contains more than 56 million parent compound-abstract relations. Found compounds, relatives, and abstracts are related to proteins in a concise ”heat map”-like overview. Compounds and proteins are highlighted in their respective abstracts, and are provided with links to PubChem and UniProt. Availability: An easy-to-use web interface with detailed descriptions, help, and statistics is available from http://cil.pharmaceuticalbioinformatics. de.
Pharma Relay 2010
Our group was proud to organize the first Pharma relay. The 30th of September was a rainy day but 8 teams followed our call of joining us ... (more infos)
This year's Eugen-Graetz-Preis was awarded to Jun. Prof. Stefan Günther, head of the Pharmaceutical Bioinformatics lab for his research work "Strukturbasierte Untersuchung von Protein-Protein-Interaktionen und deren Störung druch Kleinmoleküle"
Python & Friends 2010
At the Python & Friends Workshop 2010 in Karpacz, 20 Python bioinformaticians spent three busy days programming and learning about newest technologies. The Polish & German ISCB Student Council members brought together an equal number of people from both countries.
Some highlights of the workshop were:
- A keynote on Biopython and subsequent tutorial were given by Peter Cock. During the session, the brand new GSOC code branch for analyzing PDB structures was tested. We found the center of mass, coarse-grained models, and renumbering features working well, but the hydrogenation and SS-bond calculation require further testing.
- The K-means clustering algorithm implemented in numpy was explained in detail, and an intense numpy tutorial prepared by Bartosz Telenczuk.
- A live demonstration on how to search & cluster ligands with the Schroedinger software package was given by Ewa Bielska.
- The Galaxy tool integration workbench was in the focus of interest of many participants, and Sebastian Schultheiss gave a hands-on tutorial. A closer interaction of the Galaxy platform with Biopython would probably be useful for many people.
- In a hackathon session, a memory leak in the KDTree code of Biopython was closed.
- And of course, there was a hike into the mountains near the Czech border. The workshop took place in an informal setting bringing together groups with a variety of backgrounds. According to participants, it made sense to find out what tools are there, and to plan strategic issues like py3k migration.