CBSB08: From Computational Biophysics to Systems Biology
Workshop, 19-21 May 2008, Forschungszentrum Jülich, Germany
Scope
During the last two decades computer simulations have become an invaluable tool for researching biological systems reaching from single macromolecules to entire organisms. Examples range from folding and structural transitions in isolated proteins, the interaction between the various biomolecules, to their regulation in the cell. Future challenges will include the integration of these simulation - situated at a molecular level - into a functioning model of cells, a task that will require both new hardware and new techniques.
The workshop was organized by the John von Neumann Institute for Computing (NIC) at the Forschungszentrum Jülich, Jülich, Germany. The goal of the workshop was to bring together expertise from physics, biology, and computer science to discuss current trends in computational biophysics and systems biology. In brief, the workshop concerned the following general areas:
- Protein folding (both structure prediction and mechanics)
- 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 (CBSB08) - Proceedings
Workshop CBSB 2008, 19-21 May 2008, Jülich, Germany,
edited by Ulrich H. E. Hansmann, Jan H. Meinke, Sandipan Mohanty, Walter Nadler, Olav Zimmermann
ISBN 978-3-9810843-6-8, https://hdl.handle.net/2128/3589
NIC Series 40, July 2008, 452 pages
From Computational Biophysics to Systems Biology (CBSB08) - Proceedings (pdf, 34.7 MB)
Programme
Monday, 19 May 2008
| 07:40 | Pick up at Hotels in Jülich |
| 08:00-09:00 | Registration |
| 09:00-09:05 | Welcome by Prof. Dr. A. Bachem (CEO, FZ Jülich) |
| 09:05-09:15 | Introductory Remarks (Ulrich H.E. Hansmann, NIC-CBB) |
Morning Session (Chair: Ulrich H.E. Hansmann) | |
| 09:15-09:45 | Christoph Pospiech (IBM, Dresden, Germany): Scalable Systems for Computational Biology |
| 09:45-10:30 | Volkhard Helms (Saarland University, Saarbrücken, Germany): Computer Simulations of Protein-Protein Association in Water and at Membranes |
| 10:30-11:00 | Coffee break |
| 11:00-11:45 | Ruben Abagyan (The Scripps Research Institute, La Jolla, USA): Induced Fit in Molecular Docking |
| 11:45-12:30 | John Rice (IBM T.J. Watson Research Center, Yorktown Heights, NY, USA): High Performance Computing in Multiscale Modeling Cardiac Contraction: Bridging Proteins to Cells to Whole Heart |
| 12:30-14:00 | Lunch |
Afternoon Session (Chair: Jan Meinke) | |
| 14:00-14:45 | Henri Orland (Commissariat à l’Energie Atomique, Gif-sur-Yvette, France): Dominant Pathways in Protein Folding |
| 14:45-15:05 | Alexander Schug (University of California San Diego, San Diego, USA): Mutations as Trapdoors: The Rop-dimer with two Competing Native Conformations |
| 15:05-15:25 | Nikolay Dokholyan (University of North Carolina at Chapel Hill, Chapel Hill, USA): Simplified Approaches to Complex Biological Systems |
| 15:25-15:45 | Mai Suan Li (Polish Academy of Sciences, Warsaw, Poland): New Force Replica Exchange Method and Mechanical Unfolding of Proteins |
| 15:45-16:15 | Coffee break |
| 16:15-17:00 | Wei Yang (Florida State University, Tallahassee, FL, USA): Advancing Drug and Protein Binding Affinity Predications via Generalized Ensemble Based Methods |
| 17:00-17:20 | Iris Antes (Max-Planck-Institut für Informatik, Saarbrücken, Germany): Protein-ligand Docking Including Protein Flexibility – An Hierarchical Approach |
| 17:20-17:40 | Slawomir Orlowski (Nicolaus Copernicus University, Torun, Poland): Computer Modeling of Small Ligands Diffusion in Drosophila Melanogaster Hemoglobin |
| 17:40-18:00 | Bogdan Lesyng (University of Warsaw, Faculty of Physics, Warsaw, Poland): Protein-ligand Docking with a Two-scale Receptor Dynamics and a QM/MM Interaction Potential |
| 18:00 | Welcome Reception and Poster Session |
| 20:30 | Bus to Hotels in Jülich |
Tuesday, 20 May 2008
| 08:10 | Pickup at Hotels in Jülich |
Morning Session (Chair: Olav Zimmermann) | |
| 09:00-09:45 | Andrzej Kolinski (University of Warsaw, Warsaw, Poland): Multiscale Modeling of Protein and Protein Assemblies |
| 09:45-10:05 | Shura Hayryan (Academis Sinica, Taipei, Taiwan (ROC)): Some Aspects of RNA Folding Studied by Lattice Simulations |
| 10:05-10:25 | Kay Hamacher (TU Darmstadt, Darmstadt, Germany): Coarse-Grained Molecular Models for High-Throughput and Multi-Scale Functional Investigations |
| 10:25-11:00 | Coffee break |
| 11:00-11:45 | Ron Elber (University of Texas at Austin, Austin, USA): Atomically Detailed Simulations of Kinetics in Molecular Biophysics by Milestoning |
| 11:45-12:05 | Anton Feenstra (Free University Amsterdam, Amsterdam, The Netherlands): Predicting Protein Interactions from Functional Specificity using Multi-Relief and Multi-Harmony |
| 12:05-12:25 | Sebastian Kmiecik (Selvita, Krakow, Poland): Designing an Automatic Pipeline for Protein Structure Prediction |
| 12:25-12:40 | Group-Photo |
| 12:40-14:00 | Lunch |
Afternoon Session (Chair: Walter Nadler) | |
| 14:00-14:45 | Wilfred F. van Gunsteren (ETH Zürich, Zürich, Switzerland): Computer Simulation of Biomolecular Systems: Where Do We Stand? |
| 14:45-15:05 | Karine Voltz (German Cancer Research Center, Heidelberg, Germany): A Coarse-grained Model for the Nucleosome |
| 15:05-15:25 | Maciej Długosz (University of Warsaw, Warsaw, Poland): Interactions of Aminoglycosidic Antibiotics with the 30S Subunit - Brownian Dynamics Study |
| 15:25-15:45 | Junalyn Navarra-Madsen (TWU, Denton, USA): Coloring the Mu Transpososome |
| 15:45-16:15 | Coffee break |
| 16:15-17:00 | Roland Netz (Technical University Munich, München, Germany): Peptide Adhesion and Friction: Theoretical Approaches |
| 17:00-17:20 | Rainer Böckmann (Saarland University, Saarbrücken, Germany): Kinetics, Statistics, and Energetics of Lipid Membrane Electroporation Studied by Molecular Dynamics Simulations |
| 17:20-17:40 | Borries Demeler (The University of Texas, Health Science Center atvSan Antonio, San Antonio, Texas, USA): Modeling Conformational and Molecular Weight Heterogeneity with Analytical Ultracentrifugation Experiments (AUC) |
| 17:40-18:00 | Wolfgang Fischer (National Yang-Ming University, Taipei, Taiwan): Short Membrane Proteins from Viruses: Channel-pore Dualism? |
| 18:15 | Bus to Castle Obbendorf (Hambach) for Dinner |
| 18:30 | Dinner (Sponsored by IBM Germany) Greetings by Dr. Sebastian Schmidt, Divisional Director of Research Centre Jülich |
| 22:00 | Bus to Hotels in Jülich |
Wednesday, 21 May 2008
| 08:10 | Pickup at Hotels in Jülich |
Morning Session (Chair: Sandipan Mohanty) | |
| 09:00-09:45 | Michael Feig (Michigan State University, East Lansing, USA): Simulating Biomolecules in Cellular Environments |
| 09:45-10:05 | Giovanni La Penna (National Research Council, Sesto Fiorentino, Italy): Modelling the Free Energy of Polypeptides in Different Environments |
| 10:05-10:25 | Joachim Dzubiella (Technical University Munich, Garching, Germany): Insights from Atomistic Computer Simulations of Halophilic Proteins |
| 10:25-11:00 | Coffee break |
| 11:00-11:45 | Philippe Derreumaux (CNRS and University of Paris 7, Paris, France): Simulating the Early Steps of Amyloid Fibril Formation and Disassembly |
| 11:45-12:05 | Alfonso De Simone (University of Cambridge, Cambridge, UK): Probing the Prion Hydration by Molecular Dynamics Simulations: From Native via Misfolded to Amyloid Conformations |
| 12:05-12:25 | Volker Knecht (Max Planck Institute of Colloids and Interfaces, Potsdam, Germany): Folding and Aggregation of Model Amyloid Peptides in Explicit Solvent and at an Interface |
| 12:25-14:00 | Lunch |
Afternoon Session (Chair: Ulrich H. E. Hansmann) | |
| 14:00-14:20 | Horacio Sanchez (Forschungszentrum Karlsruhe, Eggenstein-Leopoldshafen, Germany): High Throughput in-silico Screening against Flexible Protein |
| 14:20-14:40 | Michal Wojciechowski (Polish Academy of Sciences, Warsaw, Poland): Effects of Confinement on Protein Folding |
| 14:40-15:25 | Dietmar Schomburg (Technische Universität Braunschweig, Braunschweig, Germany): Bioinformatics, Metabolomics, and Systems Biology |
| 15:25-15:30 | Concluding Remarks (Ulrich H. E. Hansmann, NIC-CBB) |
| afterwards | Bus to Cologne Social Event: Visit of a Traditional Brewhouse (drinks and food on one’s own expense) |
| 21:00 | Bus to Jülich |
Group photo
