The PostDocs Forum

Bioinformatician Abdullah Kahraman is our Featured Scientist of the Month. Read on to find out more about his research and experiences in the field.

How did you first become interested in the science field?

Learning how everything that surround us work has fascinated me since my childhood. And thus it does not come by surprise that my favourite subjects in school were chemistry and biology. I remember having spend large sums of money on scientific magazines, books and journals just to satisfy my curiosity. At the beginning my interest was very broad. Everything interested me; architecture, archeology, physics, chemistry, astronomy. At upper school however I quickly realised that my passion lies with biology.

What first inspired you to major in bioinformatics?

That computers are of upmost importance for our daily life is without any doubts. After finishing my upper school it was clear to me that I had to learn more about these grey metal boxes. But at the same time I didn’t want to give up my passion for science. Somehow just before I had to choose my undergraduate course, I received a flyer that introduced the newly established bioinformatics course at my former university. It was immediately clear to me that I had been given a unique opportunity, which I couldn’t miss.

Can you share a little bit about your research?

Protein interactions are the key mediators for cellular functions. Unfortunately, we still lack a full understanding on the principles that drive molecular interactions. Computational algorithms still struggle with the correct assessment of binding free energies in protein complexes. The hope in our lab is that chemical cross-linking experiments coupled to a mass-spectrometer will provide us with experimental constraints that will guide reliable computational modelling of protein structures and complex topologies.

What was your favorite project that you worked on?

Looking back to the various projects that I have been involved with, I think the one that I enjoyed most was the development of www.phenomicDB.de. The database was developed under the supervision of Dr. Bertram Weiss at Schering AG (today belonging to the Bayer Group) in Berlin. The database simplifies the comparison of homologous gene and their phenotypes in various organism. I got into the project just after I had finished my university lectures. Everything that I knew up to that point was more theoretical. Seeing for the first time how my knowledge took shape in form of this database was a unique experience. And not to forget of course was the great time that I had in Berlin and the friendships that I was lucky to make.

What would you advise a future bioinformatician?

Make your software available as an open-source project, no matter how bad you think it is. Any published software is much better than any publicly unavailable piece of code. I actually support the compulsory publication of software on one of the various source-code repositories for software that have been used in publications. It would ease the reproducibility of experimental results enormously.

What do you think is the most important personal characteristic for a researcher?

Curiosity, creativity and holding good knowledge in the specific research field are all important characteristics. But from my personal experience it is patience and determination that keeps a researcher going once, especially at situations where (s)he hits a seemingly unsolvable problem.

What is the best advice you could give to someone who wants to be a postdoc?

Use the opportunity to change your research topic and choose your post-doc lab wisely.

Can you share any tips for lab management and organization?

Especially in larger labs it is essential that the projects of the individuals are well defined. Otherwise competition arises which poisons the atmosphere in the lab. To boost the harmony among the group members I always found group retreats very fruitful. And a big project/goal in the lab to which everyone can contribute also can also support the communication between lab members.

Publications:
Leitner A, Walzthoeni T, Kahraman A, Herzog F, Rinner O, Beck M, & Aebersold R (2010). Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Molecular & cellular proteomics : MCP, 9 (8), 1634-49 PMID: 20360032

Kahraman A, Morris RJ, Laskowski RA, Favia AD, & Thornton JM (2010). On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins. Proteins, 78 (5), 1120-36 PMID: 19927322

Kahraman A, Morris RJ, Laskowski RA, & Thornton JM (2007). Shape variation in protein binding pockets and their ligands. Journal of molecular biology, 368 (1), 283-301 PMID: 17337005

Kahraman A, Avramov A, Nashev LG, Popov D, Ternes R, Pohlenz HD, & Weiss B (2005). PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics. Bioinformatics (Oxford, England), 21 (3), 418-20 PMID: 15374875