Bioinformatics 2008 Conference 24-27 April, 2008 Warsaw, Poland,
Bioinformatics 2008 will be the 10th conference in a series organized by by the Society for Bioinformatics in Northern Europe. Bioinformatics 2008 is organized by Interdisciplinary Centre for Mathematical and Computational Modelling. It will be held on the campus of the University of Warsaw

 

SCIENTIFIC PROGRAMME

Thursday 24 April
Morning-Noon:

Arrival and registration.

Early afternoon:

Conference opening,

Keynote lecture I - Janet Thorton (EBI, UK)

Afternoon:

Session I (invited speakers)

"Evolution of Regulatory Networks" (chair: Mikhail Gelfand)
- Sarah Teichmann (Cambridge University, UK)
- Philipp Bucher (ISEC, Lausanne, Switzerland)
- Michael Laessig (University of Cologne, Germany)
- Paramvir Dehal (Lawrence Berkeley National Laboratory)

Evening:

Reception + Poster Session

Friday 25 April

Morning:

Session II (invited speakers)

"Structural Bioinformatics of RNA" (chair: Janusz M. Bujnicki)
- Eric Westhof (University of Strasbourg, France)
- Ye Ding (Wadsworth Center, USA)
- François Major (Université de Montréal, Canada)
- Kevin Sanbonmatsu (LANL, USA)

Early afternoon:

Keynote II: Andrzej Kolinski (University of Warsaw, Poland)

Afternoon :

Session III (invited speakers)

"Protein Structure Prediction" (chair: Ceslovas Venclovas)
- Janusz M. Bujnicki (IIMCB, Warsaw & UAM, Poznan, Poland)
- Keith Dunker, (Indiana University)
- Jianpeng Ma (Baylor College of Medicine & Rice University, Houston, USA)
- Dr Michael Tyka (University of Washington, USA)

Evening:

Poster Session

Saturday 26 April

Morning:

Session IV (invited speakers)

"Machine Learning in Bioinformatics" (chair: Jan Komorowski)
- Yves Moreau (University of Leuven, Belgium)
- Andrey Rzhetsky (Columbia University, USA)
- Ross King (University of Wales, Aberystwyth, UK)
- Lucila Ohno-Machado (Harvard Medical School, USA)

Early afternoon:

Keynote lecture III: Gunnar von Heijne (Stockholm Center for Biomembrane Research,
Sweden)

Oral presentation of selected posters I

Evening:

Conference dinner

Sunday 27 April

Morning:

Session V (invited speakers)

"Bioinformatics of Membrane Proteins" (chair: Arne Elofsson)
- Mark Sansom (University of Oxford, UK)
- James Bowie (UCLA, USA),
- David Jones (UCL, London, Great Britain),
- Rita Casadio (University of Bologna, Italy),

Early Afternoon:

Oral presentation of selected posters II

Evening:

Departure

Recently, we’ve performed series of protein folding pathway simulations by the use of CABS, reduced protein-modeling tool. Results have been just published in PNAS. The correspondence between the simulation and experiment shows that knowledge-based, statistical potentials are not only useful in protein structure predictions but are also capable of reproducing the folding pathways. Thus, the results of this work significantly extend the applicability range of reduced models in the theoretical study of proteins.

Try our procedure for protein reconstruction from alpha carbon coordinates and subsequent models assessment suited for the high-resolution structure prediction. Methods constituing the procedure, can be effectively used in a large-scale computations.

The procedure compose of the three following steps:

• protein backbone reconstruction by the use of BBQ - an algorithm for protein backbone reconstruction that comprises very high computational efficiency with high accuracy. Details can be found in the publication: D. Gront, S. Kmiecik, A. Kolinski Backbone Building from Quadrilaterals. A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. J. Comput. Chemistry 28(9):1593-1597, 2007
• side chains reconstruction which should be performed as accurate as possible by one of the available methods adjusting side chain rotamers to the existing backbone e.g. SCWRL
• protein models assessment by the use of Molecular Mechanics with fixed alpha carbons to rank-order the all-atom models built on the scaffolds of the reduced models. Details can be found in the publication: S. Kmiecik, D. Gront, A. Kolinski. Towards high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field. BMC Structural Biology 7:43, 2007

The procedure can be effectively used in a large-scale studies:

• after reduced modeling stage either as a final step in protein structure prediction protocol or in multiscale studies of protein dynamics
• when structures from different sources (and of different quality) are being compared

Check our website section "Slides & Presentations" (menu: Files) for upcoming seminar presentations. Recently, Dr Dominik Gront seminars on "Selected topics in Monte Carlo methods", have been added.

>> go to "Slides & Presentations"

New tool, BBQ was added to our services. BBQ is a program for protein backbone reconstruction from C alpha trace that comprises very high computational efficiency with high accuracy.
Check also for updates of BioShell package. BioShell is a suite of programs designed for pre- and post-processing in protein structure modeling protocols. The package provides a convenient set of tools for conversion between various sequence and structure formats. It is also possible to calculate simple properties of protein conformations.

For more details, click on the appropriate banner: