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From Computational Biophysics to Systems Biology

May 19 - 21 2008, Jülich, Germany



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



Monday 19.05.2008

07:40Pick up at Hotels in Jülich
09:00-09:05Welcome by Prof. Dr. A. Bachem (CEO, FZ Jülich)
09:05-09:15Introductory Remarks (Ulrich H.E. Hansmann, NIC-CBB)

Morning Session (Chair: Ulrich H.E. Hansmann)

09:15-09:45Christoph Pospiech (IBM, Dresden, Germany):
Scalable Systems for Computational Biology
09:45-10:30Volkhard Helms (Saarland University, Saarbrücken, Germany):
Computer Simulations of Protein-Protein Association in Water and at Membranes
10:30-11:00Coffee break
11:00-11:45Ruben Abagyan (The Scripps Research Institute, La Jolla, USA):
Induced Fit in Molecular Docking
11:45-12:30John 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

Afternoon Session (Chair: Jan Meinke)

14:00-14:45Henri Orland (Commissariat à l’Energie Atomique, Gif-sur-Yvette, France):
Dominant Pathways in Protein Folding
14:45-15:05Alexander Schug (University of California San Diego, San Diego, USA):
Mutations as Trapdoors: The Rop-dimer with two Competing Native Conformations
15:05-15:25Nikolay Dokholyan (University of North Carolina at Chapel Hill, Chapel Hill, USA):
Simplified Approaches to Complex Biological Systems
15:25-15:45Mai Suan Li (Polish Academy of Sciences, Warsaw, Poland):
New Force Replica Exchange Method and Mechanical Unfolding of Proteins
15:45-16:15Coffee break
16:15-17:00Wei Yang (Florida State University, Tallahassee, FL, USA):
Advancing Drug and Protein Binding Affinity Predications via Generalized Ensemble Based Methods
17:00-17:20Iris Antes (Max-Planck-Institut für Informatik, Saarbrücken, Germany):
Protein-ligand Docking Including Protein Flexibility – An Hierarchical Approach
17:20-17:40Slawomir Orlowski (Nicolaus Copernicus University, Torun, Poland):
Computer Modeling of Small Ligands Diffusion in Drosophila Melanogaster Hemoglobin
17:40-18:00Bogdan Lesyng (University of Warsaw, Faculty of Physics, Warsaw, Poland):
Protein-ligand Docking with a Two-scale Receptor Dynamics and a QM/MM Interaction Potential
18:00Welcome Reception and Poster Session
20:30Bus to Hotels in Jülich

Tuesday 20.05.2008

08:10Pickup at Hotels in Jülich

Morning Session (Chair: Olav Zimmermann)

09:00-09:45Andrzej Kolinski (University of Warsaw, Warsaw, Poland):
Multiscale Modeling of Protein and Protein Assemblies
09:45-10:05Shura Hayryan (Academis Sinica, Taipei, Taiwan (ROC)):
Some Aspects of RNA Folding Studied by Lattice Simulations
10:05-10:25Kay Hamacher (TU Darmstadt, Darmstadt, Germany):
Coarse-Grained Molecular Models for High-Throughput and Multi-Scale Functional Investigations
10:25-11:00Coffee break
11:00-11:45Ron Elber (University of Texas at Austin, Austin, USA):
Atomically Detailed Simulations of Kinetics in Molecular Biophysics by Milestoning
11:45-12:05Anton Feenstra (Free University Amsterdam, Amsterdam, The Netherlands):
Predicting Protein Interactions from Functional Specificity using Multi-Relief and Multi-Harmony
12:05-12:25Sebastian Kmiecik (Selvita, Krakow, Poland):
Designing an Automatic Pipeline for Protein Structure Prediction

Afternoon Session (Chair: Walter Nadler)

14:00-14:45Wilfred F. van Gunsteren (ETH Zürich, Zürich, Switzerland):
Computer Simulation of Biomolecular Systems: Where Do We Stand?
14:45-15:05Karine Voltz (German Cancer Research Center, Heidelberg, Germany):
A Coarse-grained Model for the Nucleosome
15:05-15:25Maciej Długosz (University of Warsaw, Warsaw, Poland):
Interactions of Aminoglycosidic Antibiotics with the 30S Subunit - Brownian Dynamics Study
15:25-15:45Junalyn Navarra-Madsen (TWU, Denton, USA):
Coloring the Mu Transpososome
15:45-16:15Coffee break
16:15-17:00Roland Netz (Technical University Munich, München, Germany):
Peptide Adhesion and Friction: Theoretical Approaches
17:00-17:20Rainer Böckmann (Saarland University, Saarbrücken, Germany):
Kinetics, Statistics, and Energetics of Lipid Membrane Electroporation
Studied by Molecular Dynamics Simulations
17:20-17:40Borries 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)
17:40-18:00Wolfgang Fischer (National Yang-Ming University, Taipei, Taiwan):
Short Membrane Proteins from Viruses: Channel-pore Dualism?
18:15Bus to Castle Obbendorf (Hambach) for Dinner
18:30Dinner (Sponsored by IBM Germany)
Greetings by Dr. Sebastian Schmidt, Divisional Director of Research Centre Jülich
22:00Bus to Hotels in Jülich

Wednesday 21.05.2008

8:10Pickup at Hotels in Jülich

Morning Session (Chair: Sandipan Mohanty)

09:00-09:45Michael Feig (Michigan State University, East Lansing, USA):
Simulating Biomolecules in Cellular Environments
09:45-10:05Giovanni La Penna (National Research Council, Sesto Fiorentino, Italy):
Modelling the Free Energy of Polypeptides in Different Environments
10:05-10:25Joachim Dzubiella (Technical University Munich, Garching, Germany):
Insights from Atomistic Computer Simulations of Halophilic Proteins
10:25-11:00Coffee break
11:00-11:45Philippe Derreumaux (CNRS and University of Paris 7, Paris, France):
Simulating the Early Steps of Amyloid Fibril Formation and Disassembly
11:45-12:05Alfonso De Simone (University of Cambridge, Cambridge, UK):
Probing the Prion Hydration by Molecular Dynamics Simulations:
From Native via Misfolded to Amyloid Conformations
12:05-12:25Volker Knecht (Max Planck Institute of Colloids and Interfaces, Potsdam, Germany):
Folding and Aggregation of Model Amyloid Peptides in Explicit Solvent and at an Interface

Afternoon Session (Chair: Ulrich H. E. Hansmann)

14:00-14:20Horacio Sanchez (Forschungszentrum Karlsruhe, Eggenstein-Leopoldshafen, Germany):
High Throughput in-silico Screening against Flexible Protein
14:20-14:40Michal Wojciechowski (Polish Academy of Sciences, Warsaw, Poland):
Effects of Confinement on Protein Folding
14:40-15:25Dietmar Schomburg (Technische Universität Braunschweig, Braunschweig, Germany):
Bioinformatics, Metabolomics, and Systems Biology
15:25-15:30Concluding Remarks (Ulrich H. E. Hansmann, NIC-CBB)
afterwardsBus to Cologne
Social Event: Visit of a Traditional Brewhouse (drinks and food on one’s own expense)
21:00Bus to Jülich

Participants of CBSB08