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CBSB06: From Computational Biophysics to Systems Biology
Workshop, 6-9 June 2006, Forschungszentrum Jülich, Germany
Start
6th June 2006 07:00 AM
End
9th June 2006 06:30 PM
Scope
Over the last few decades the scope of biology has changed from categorizing experimental observations to understanding the underlying mechanisms. This is at least in part due to the increasing use of computers. Computers allow us to study single macromolecules, the interaction between various biomolecules, or their regulation in the cell. For many medical and pharmaceutical applications such as the understanding of desease pathways or the working of drugs at the level of an individual cell one would like an integration of these simulations - situated at a molecular level - into a functioning model of cells. This is one of the big challenges in computational biology requiring both new hardware and new techniques.
The many benefits of such an extension of computational biophysics into systems biology motivated the workshop that the research group "Computational Biology and Biophysics" held June 6-9, 2006 at the John von Neumann Institute for Computing in Jülich, Germany. Specifically, the workshop targeted the following general areas at the interface between (computational) biophysics and systems biology:
- Protein folding (both structure prediction and mechanics)
- Mis-folding and aggregation
- Interaction between proteins and other molecules
- Assembly of nano-structures, multi-protein, protein-DNA/RNA complexes
Cellular systems at the molecular level
Proceedings
From Computational Biophysics to Systems Biology 2006 - Proceedings
Workshop CBSB 2006, 06-09 June 2006, Jülich, Germany
edited by Ulrich H. E. Hansmann, Jan H. Meinke, Sandipan Mohanty, Olav Zimmermann
ISBN 978-3-9810843-0-6, https://hdl.handle.net/2128/2944
NIC Series 34, September 2006, 224 pages
From Computational Biophysics to Systems Biology (CBSB06) - Proceedings (pdf, 11.9 MB)
Programme
Tuesday, 6 June 2006
| 08:00 | Pick up in Aachen |
| 09:00 | Registration |
| 10:00 - 10:15 | "Supercomputing at NIC", Thomas Lippert, Director NIC |
| 10:15 - 10:30 | "From Computational Biophysics to Systems Biology", Ulrich Hansmann |
Morning Session (Chair: U.H.E Hansmann) | |
| 10:30 - 11:30 | Harold Scheraga, The Two Aspects of the Protein Folding Problem |
| 11:30 - 11:40 | Organizational remarks |
| 11:40 - 12:00 | Coffee break |
| 12:00 - 12:30 | Adam Liwo, Optimization of the united-residue UNRES force field for Langevin dynamics |
| 12:30 - 14:00 | Lunch |
Afternoon Session (Chair: J.H. Meinke) | |
| 14:00 - 14:45 | Tetsu Narumi, A High-Speed Special-Purpose Computer for Molecular Dynamics Simulations: MDGRAPE-3 |
| 14:45 - 15:15 | Cezary Czaplewski, Multiplexed-replica exchange molecular dynamics with UNRES force-field as an effective method for exploring the conformational energy landscape of proteins |
| 15:15 - 15:45 | Coffee break |
| 15:45 - 16:15 | Mariusz Makowski, Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. Tests with simple spherical systems |
| 16:15 - 16:45 | Stanislaw Oldziej, Optimizing the UNRES force field for the prediction of proteins |
| 16:45 - 17:15 | Michael Bachmann, Reduction to the simplest - The complexity of minimalistic heteropolymer models |
| 17:15 - 17:45 | Dominik Gront, High accuracy method to protein backbone reconstruction |
| 18:00 - 20:00 | Welcome Reception |
| 20:00 | Bus to Aachen |
Wednesday, 7 June 2006
| 08:00 | Pick up in Aachen |
Morning Session (Chair: T. Narumi) | |
| 09:00 - 9:45 | Wolfgang Wenzel, De novo protein structure prediction and folding |
| 09:45 - 10:15 | Martin Mönnigmann, Protein Loop Structure Prediction With Flexible Stem Geometries |
| 10:15 - 10:45 | Walter Nadler, Molecular Transport Through Channels and Pores: Effects of In-Channel Interactions and Blocking |
| 10:45 - 11:15 | Coffee break |
| 11:15 - 12:00 | Gordon Crippen, Cluster Distance Geometry and Protein Folding |
| 12:00 - 12:30 | Giovanni La Penna, Modelling protein-DNA interactions in chromatin |
| 12:30 - 14:00 | Lunch |
Afternoon Session (Chair: Adam Liwo) | |
| 14:00 - 14:45 | Anders Irbäck, Protein folding and aggregation studied using an all-atom model with a simplified energy function |
| 14:45 - 15:15 | Inta Liepina, Molecular dynamics study of two ABL-SH3 domain peptides amyloid formation |
| 15:15 - 15:45 | Coffee break |
| 15:45 - 16:15 | Siegfried Höfinger, A Very General Solvation Model for BioMolecular Simulation |
| 16:15 - 16:45 | Magdalena Gruziel, From microscopic Monte-Carlo simulations to macroscopic solvation models |
| 17:00 - 19:00 | Poster Session (beverages and snacks provided) |
| 19:00 | Bus to Aachen |
Thursday, 8 June 2006
| 08:00 | Pick up in Aachen |
Morning Session (Chair: A. Irbäck) | |
| 09:00 - 09:30 | Matthias Stein, Integrating Structural and Kinetic Enzymatic Information in Systems Biology |
| 09:30 - 10:00 | Jesus Izaguirre, Inferring Protein-Protein Interactions from Data and Domain Docking |
| 10:00 - 10:45 | Roland Eils, Computational Systems Biology |
| 10:45 - 11:15 | Coffee break |
| 11:15 - 11:45 | Anton Feenstra, Sub-type Specific Sites for SMAD Receptor Binding Identified by Sequence Comparison using "Sequence Harmony" |
| 11:45 - 12:15 | Daniele Dell'Orco, In silico screening of mutational effects on Enzyme-Inhibitor affinity: a docking-based approach |
| 12:15 - 12:45 | Francesco Guerrieri, Ab initio simulations of the Cu binding sites on the N-terminal |
| 12:45 - 14:00 | Lunch |
Afternoon Session (Chair: O. Zimmermann) | |
| 14:00 - 14:45 | Ruhong Zhou, Dewetting Transition and Hydrophobic Collapse in Protein Aggregates |
| 15:00 | Leaving for Aachen |
| 15:45 | Tour of the cathedral |
| 17:30 | Tour of downtown Aachen |
| 19:00 | Dinner in Aachen |
Friday, 9 June 2006
| 08:00 | Pick up in Aachen |
Morning Session (Chair: G. Crippen) | |
| 09:00 -9:45 | Yuko Okamoto, Generalized-Ensemble Algorithms and Membrane Protein Structure Predictions |
| 09:45 - 10:15 | Yuguang Mu, A new method of replica exchange method for protein folding in explicit water |
| 10:15 - 10:45 | Caroline Taylor, Using simple fluid wetting as a model for cell spreading |
| 10:45 - 11:15 | Coffee break |
| 11:15 - 12:00 | A. Kolinski, Modeling protein structure, dynamics and thermodynamics with reduced representation of conformational space |
| 12:00 - 12:30 | Wolfhard Janke, Adsorption phenomena at organic-inorganic interfaces |
| 12:30 - 14:00 | Lunch |
Afternoon Session (Chair: U.H.E. Hansmann) | |
| 14:00 - 14:30 | Phanourios Tamamis, Conformational analysis of compstatin with molecular dynamics simulations in explicit water |
| 14:30 - 15:15 | Avijit Ghosh, From Simulation to Therapy: A Systems Biology Approach to Oncogene Detection and Drug Design |
| 15:15 - 15:45 | Coffee break |
| 15:45 - 16:30 | Social: Opening game of the World Cup 2006 Germany against Costa Rica (Begin 18:00 ZDF) |
| 20:30 | Bus to Aachen leaves after the game (Return to Aachen in time to watch Poland vs. Ecuador) |
Last Modified: 05.11.2022