Research | Where | HowTo | Links | Home Martin Mann

Theoretical Biochemistry Group
University of Vienna

Phone: +43-1-4277-52742
Fax: +43-1-4277-52793

Research and Interests

• energy landscapes of biopolymer models
• computational chemistry
• simplified protein models
• protein structure prediction
• constraint programming
• object oriented programming

Software and Information



• I am one of the distributors of the Energy Landscape Library (ELL) and the BIU library.
• My CPSP-tools enable studies for HP-type protein models in complex 3D-lattices.
• The LatPack is made for studies in arbitrary lattice protein models.
• LatFit allows for lattice approximations/fits or real protein structures in PDB format.
• To avoid ugly learning by trying: my HowTo-site.
• For Constraint Programming I am using and extending the Gecode C++ library.
• For some usefull free tools have a look here.

Collaborations

To be successful you need a team. Therefore I am happy to collaborate with ...


• Bela Bender from IWW - University of Freiburg (Germany) on the mapping of tree growth onto weather data.
• Fabrizio Costa from University of Freiburg (Germany) on machine learning in chemistry.
• Alessandro Dal Palu from University of Parma (Italy) on the application of constraint programming in lattice protein models.
• Christoph Flamm and Alexander Ullrich from University of Vienna (Austria) and Leipzig (Germany) on graph grammars and their applications.
• Konstantin Klemm from University of Leipzig (Germany) on energy landscapes and their properties.
• Rhodri Saunders and Charlotte Deane from University of Oxford (UK) on co-translational folding of proteins.
• Kathleen Steinhöfel, Leonidas Kapsokalivas, and Dayem Ullah from King's College London (UK) on new folding simulation techniques for lattice protein models.
• Guido Tack from Saarland University (Germany) to integrate AND/OR search into Gecode.
• Michael T. Wolfinger from University of Vienna (Austria) about energy landscapes of lattice proteins.
• Stephané Zampelli from Université Catholique de Louvain (Belgium) about CP-based graph matching algorithms.
• I have been supported and part of the EU project EMBIO working on energy landscapes of lattice proteins.

Publications and Teaching

• Here is my list of publications.
• Also a list including my posters is available.
• An introductory talk on Lattice proteins, CPSP approach, and applications I presented.
  
  
• At the Bioinformatics group at the University Freiburg:
  
  • I was responsible for the exercise course of the special lecture on 'Protein folding and energy landscapes' ( SS'09 ),
  • as well as the exercise course of the 'Bioinformatics I' lecture ( SS'10 ).
  • I was supervising a Java programming course about bioinformatics algorithms ( WS'09, '08, '07, '06 ) and a Perl course ( SS'08 )
  • Further, I am the mentor of several theses and student projects.

Where to meet?

2011 ...

not yet clear where next ;)

... I'll go to!

And I' ve been to ...



... 2011	... 2010
Our workshop in Freiburg, Germany (April '11) TBI Winterseminar in Bled, Slovenia (Feb. '11)	TBI in Vienna, Austria (Nov. '10) Bioinformatics Group in Leipzig, Germany (Aug. '10) ISMB'10 in Boston, USA (July '10) Our workshop in Freiburg, Germany (April '10) DPG Regensburg 2010, Germany (March '10) TBI Winterseminar in Bled, Slovenia (Feb. '10)

About me ...

Currently, I am a PostDoc assistent at the
Theoretical Biochemistry (TBI) group
at the University of Vienna, Austria.

I was born and grew up in Erfurt. For my studies
at the Friedrich-Schiller-University Jena
I got my diploma in Bioinformatics March 2006.
In June 2011, I received my doctorate from the
Albert-Ludwigs-University Freiburg, Germany,
working at Prof. Backofen's Bioinformatics group.

Most important things? Mhh.. mails of course! ;)

Because they connect everything: friends, sports,
journeys and all the remaining stuff I love!