Preface
U. H. E. Hansmann, J. H. Meinke, S. Mohanty, W. Nadler,
O. Zimmermann
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Invited Talks |
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Strategies to Overcome the Induced Fit Effects in Molecular Docking
I. Kufareva, R. Abagyan |
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Simulating the Early Steps of Amyloid Fibril Formation and Disassembly
Ph. Derreumaux |
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Milestoning
R. Elber, A. West |
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Simulating Biomolecules in Cellular Environments
M. Feig, S. Tanizaki, J. Chocholoušová, M. Sayadi, J. W. Clifford, B. D. Connelly, S. Mukherjee, S. M. Law |
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Scalable Systems for Computational Biology
Ch. Pospiech |
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High Performance Computing in Multiscale Modeling Cardiac Contraction: Bridging Proteins to Cells to Whole Heart
J. J. Rice |
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Determination of Protein Structure in Solution
Based on 13CαChemical Shifts and NOE Distance Constraints
J. A. Vila, H. A. Scheraga |
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Computer Simulation of Biomolecular Systems: Where Do We Stand?
W. F. van Gunsteren, D. P. Geerke |
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Towards Accurate Predictions of Binding Affinities: The Simulated Scaling Based Free Energy Method
L. Zheng, H. Li, W. Yang |
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Contributed Talks |
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Protein-Ligand Docking Including Protein Flexibility: A Hierarchical Approach
I. Antes, Ch. Hartmann, Th. Lengauer |
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Electroporation Studied by Molecular Dynamics Simulations
R. A. Böckmann, S. W. I. Siu, S. Leis, B. L. de Groot, S. Kakorin, E. Neumann, H. Grubmüller |
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Modeling Conformational and Molecular Weight Heterogeneity with Analytical Ultracentrifugation Experiments
B. Demeler, E. Brookes |
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Exploring the Free Energy Surface of Short Peptides by Using Metadynamics
C. Camilloni, A. De Simone |
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Association of Neamine and its Derivative with the Ribosomal A-Site RNA
M. Długosz, J. Trylska |
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Simplified Approaches to Complex Biological Systems
N. V. Dokholyan |
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Predicting Protein Interactions from Functional Specificity
K. A. Feenstra, G. Bastianelli, J. Heringa |
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Short Membrane Proteins from Viruses: Channel-Pore Dualism?
G. Patargias, H. Martay, J. Krüger, C.-P. Chen, Y.-T. Wang, M.-D. Lee, C.-C. Chen, G.-S. Hong, W. B. Fischer |
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Coarse-Grained Molecular Models for High-Throughput and Multi-Scale Functional Investigations
K. Hamacher |
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Simulation of RNA Folding on the Simple Cubic Lattice
S. Hayryan, K. G. Sargsyan,C.-K. Hu |
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Designing an Automatic Pipeline for Protein Structure Prediction
S. Kmiecik, M. Jamroz, A. Zwolinska, P. Gniewek, A. Kolinski |
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Conformational Polymorphism of a Fibrillogenic Fusion Peptide in Explicit Solvent and at an Interface
V. Knecht, R. Lipowsky |
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Modeling the Free Energy of Polypeptides in Different Environments
G. La Penna, S. Furlan, A. Perico |
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Protein-Ligand Docking with Two-Scale Receptor Dynamics and QM/MM Potential
J. A. Kalinowski, B. Lesyng |
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Inhibition of Fibril Formation of Beta-Amyloid Peptides
N. S. Lam, M. Kouza, H. Zung, M. S. Li |
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A Topological Model of a "Jumping Gene" Machine
J. Navarra-Madsen |
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Computer Modeling of Small Ligands Diffusion in Drosophila Melanogaster Hemoglobin
L. Dams, S. Orlowski, W. Nowak |
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High Throughput In-Silico Screening Against Flexible Protein Receptors
H. Sánchez, B. Fischer, H. Merlitz, W. Wenzel |
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Mutations as Trapdoors: The Rop-Dimer with Two Competing Native Conformations
A. Schug, J. Onuchic |
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Global Motions in the Nucleosome Explored Using a Coarse-Grained Model
K. Voltz, J. Trylska, V. Tozzini, V. Kurkal-Siebert, J. C. Smith, J. Langowski |
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Effects of Confinement and Crowding in Protein Folding
M. Wojciechowski, M. Cieplak |
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Posters |
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Conformational Study of Alzheimer's Aβ Wild Type Peptide and Flemish Mutant
P. Anand, F. S. Nandel, U. H. E. Hansmann |
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Effect of Temperature on the Structural and Hydrational
Properties of Human Islet Amyloid Polypeptide in Water
M. N. Andrews, I. Brovchenko, R. Winter |
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A Knowledge-Based Potential for Protein-RNA Docking
R. P. Bahadur, M. Zacharias |
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Fast and Accurate Structure-Based Calculation of Folding Free Energies and Binding Affinities
C. M. Becker, A. Benedix, B. L. de Groot, A. Caflisch, R. A. Böckmann |
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Correlation Effects in Protein-Protein Recognition
H. Behringer, F. Schmid |
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Prediction of Twist of Amyloid Fibrils Using Molecular Dynamics
J. Berryman, S. Radford, S. Harris |
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Automatic Sequential NOESY Assignment and NMR Structure Improvement by X-Ray
K. Brunner, W. Gronwald, A. Fischer, J. Trenner, K.-P. Neidig, H. R. Kalbitzer |
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Exploring the First Steps of Aβ16-22 Protofibril Disassembly by N-Methylated Inhibitors
Y. Chebaro, Ph. Derreumaux |
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Simulation of the Outer Membrane Protein X in a Lipid Bilayer and in a Micelle
A. Choutko, A. Glättli, W. van Gunsteren |
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OPERA: An OPtimized coarse-grained Energy model for RnA
C. Colas, P. H. Nguyen, J.-Ch. Gelly, Ph. Derreumaux |
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Understanding of High Pathogenicity of the Avian Influenza Virus H5N1: Why H5 is Better Cleaved by Furin
P. Decha, P. Wolschann, S. Hannongbua |
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Bound Water as a Tool to Detect Soluble Amyloid Oligomers and Amyloid Protofibrils, the Early Stage of Development of the Alzheimer's Disease
F. Despa |
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Stabilizing Regions in Membrane Proteins
F. Dressel, A. Marsico, A.Tuukkanen, R. Winnenburg, M. Schroeder, D. Labudde |
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Loop Parameterization and RNA Secondary Structure Folding
T. R. Einert, P. Näger, H. Orland, R. R. Netz |
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Investigation of Structure of Amphipathic Peptides in Different Environments via Replica Exchange Molecular Dynamics Simulations
Ö. Engin, M. Sayar |
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Protein-Protein Interaction Prediction
F. Fink, St. Ederer, W. Gronwald |
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Determining RNA Flexibility by Graph Theory: Ribosomal Exit Tunnel as a Case Study
S. Fulle, H. Gohlke |
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Ab initio Molecular Dynamics of the Zn-Binding Site of the Alzheimer's Amyloid β-Peptide
S. Furlan, G. La Penna |
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Do Amyloidogenic Regions Intersect with Folding Nuclei of Native Structure?
O. V. Galzitskaya |
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Coarse-Grained Simulations of Protein Adsorption on Solid Surfaces
B. Griepernau, Ch. Hanke, L. Santen, R. A. Böckmann |
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Towards Understanding the Early Events in the Conformational Transition of Amyloid Beta Peptides
S. Hayat, V. Helms |
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Protein Interactions with their Environment
M. Hoefling, K. E. Gottschalk |
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Identification of Differential Protein Expression in Response to the Application of BioRegulators that Enhance Plant Productivity and Quality
R. Horn, D. Zimmermann, St. Schillberg |
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Hamiltonian Replica Exchange Molecular Dynamics Using Soft-Core Interactions to Enhance Conformational Sampling
J. Hritz, Ch. Oostenbrink |
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TollML: A Database of Toll-Like Receptor Structural Motifs
F. Jamitzky, J. Gong, T. Wei, W. M. Heckl, S. C. Rössle |
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The Glucan, Water Dikinase - A Kinetic Model to Understand the Initial Step in Starch Mobilization in Plant Leaves
Ö. Kartal, O. Ebenhöh |
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Engrailed Homeodomain Folds Overnight by 100 Processors
K. V. Klenin, W. Wenzel |
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Single Molecule FRET Study of the Conformational Energy Landscape of a Transfer RNA
A. Yu. Kobitski, M. Hengesbach, M. Helm, G. U. Nienhaus |
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Impact of Induced Fit on Ligand Scoring and a Strategy of Identifying a Minimal Set of Flexible Residues
D. Kokh, W. Wenzel |
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Contributions to the Hydration Free Energies of Amino Acids
G. König, St. Boresch |
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Conservation Analysis of Functional Important Residues of the Oxygen Evolving Mechanism Located in the D1 Subunit of Photosystem II
E.-M. Krammer, G. M. Ullmann |
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Viral Membrane Proteins: Flexibility and Assembly
J. Krüger, W. B. Fischer |
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Hen Egg White Lysozyme Adsorption on a Mica Surface:
A Fully Atomistic Molecular Dynamics Study
K. Kubiak, P. Mulheran |
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Internal Dynamics of Ribosomal Elongation Factors G and Tu Studied with All-Atom and Coarse-Grained Molecular Dynamics
K. Kulczycka, M. Długosz, J. Trylska |
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Efficient Molecular Docking of Drug Molecules into DNA Targets and their Enrichment by Cutting-Edge Technologies
S. A. Kumar, M. Petersen, M. G. B. Drew, M. M.-L. Grage, C. J.
Cardin, Y. Gan |
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Applications of a Novel Biasing Potential to Study DNA Translocation and DNA Base Flipping
S. M. Law, M. Feig |
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Characterization of the Quinolone-Gyrase-Interaction Using Docking, Molecular-Dynamics and Site-Directed Mutagenesis
J. Lenz, Th. Lemcke, P. Heisig, A. Torda |
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Classification of Kinases: A Fast, Automated Structure-Based Approach
J. Lenz, Th. Margraf, Th. Lemcke, A. Torda |
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Modelling of Possible Binding Modes of Caffeic Acid Derivatives to JAK3 Kinase
J. Kuska, P. Setny, B. Lesyng |
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Looking for Inhibitors of RIO Kinases
M. Geller, Ł. Walewski, M. Długosz, B. Lesyng |
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1.4-DHP-Lipid Forms a Tubular Micellae
I. Liepina, C. Czaplewski, V. Ose, R. Danne, G. Duburs |
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Protein Structure Prediction Using Coarse Grain Force Fields
N. Mahmood, A. Torda |
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HANSWURST: Fast Efficient Multiple Protein Structure Alignments
Th. Margraf, A. Torda |
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Computer Simulations of Product Dissociation from the Active Site of the Anthrax Edema Factor
L. Martínez, Th. Malliavin, M. Nilges, A. Blondel |
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A Software Library for Monte Carlo-Based Rigid Body Modelling Against Small Angle Scattering Data
Ch. Meesters |
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Development of a Docking Methodology for Predicting the Structure of Protein-Protein Complexes
I. Meliciani, S. M. Gopal, W. Wenzel |
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A Non-Native Helix Extension Channels Folding
S. Mohanty, U. H. E. Hansmann |
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Modulation of Aggregate Size and Shape Distributions of Amyloid-β Peptide Solutions by a Designed β-Sheet Breaker
L. Nagel-Steger, B. Demeler, K. Hochdörffer, Th. Schrader, D. Willbold |
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Flexible Peptide-Protein Docking Employing PSO@Autodock
V. Namasivayam, R. Günther |
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Exploration of the Energy Landscape of Protein-Protein and Antibody-Antigen Interactions
J. Neumann, J. Morfill, K. E. Gottschalk |
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From Isotope Labeling Patterns to Metabolic Flux Rates
K. Nöh, M. Weitzel, W. Wiechert |
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The Inherent Stability of Collagen
V. K. Pálfi, A. Perczel |
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Molecular Dynamics Simulations of the Metaloenzyme Thiocyanate Hydrolase with Non-Corrinoid Co(III) in Active Site
L. Peplowski, W. Nowak |
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Constraint Network Analysis: Exploiting the Link Between Protein Rigidity and Thermostability
S. Radestock, H. Gohlke |
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Solvent in Protein Interfaces: Molecular Dynamics Approach
S. Samsonov, J. Teyra, M. T. Pisabarro |
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Nearly-Deterministic Methods for Optimising Protein Geometry
G. Schenk, A. Torda |
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Different Types of Protein Folding Identified with a Coarse-Grained Heteropolymer Model
St. Schnabel, M. Bachmann, W. Janke |
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Effect of Surfaces on the Aggregation of Hydrophobic and Hydrophilic Amyloidogenic Peptides
G. Singh, I. Brovchenko, R. Winter |
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Free Energy Study of Ion Permeation through Gramicidin
S. W. I. Siu, R. A. Böckmann |
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Free-Energy Based All-Atom Protein Folding Using Worldwide Distributed Computational Resources
T. Strunk, S. M. Gopal, K. Klenin, W. Wenzel |
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Parallel 2d-Wavelet Transform on the Cell/B.E. for Fast
Calculation of Coulomb Potentials
A. Schiller, G. Sutmann |
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RedMD - A New Package for Reduced Molecular Dynamics
M. Szypowski, A. Górecki, J. Trylska |
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Insights into the Self-Assembly of Phenylalanine Oligopeptides by Replica Exchange MD Simulations with the GBSW Implicit-Solvent Model
P. Tamamis, L. Adler-Abramovich, E. Gazit, G. Archontis |
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Analysis and Classification of the Structural Interactome
J. Teyra, M. Paszkowski-Rogacz, G. Anders, M. T. Pisabarro |
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Characterization of the Binding Surface of the Human Protein GABARAP
Y. Thielmann, O. H. Weiergräber, J. Mohrlüder, B. W. Koenig, R. Hartmann, Th. Stangler, K. Wiesehan, D. Willbold |
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Freezing and Collapse of Flexible Polymers
Th. Vogel, M. Bachmann, W. Janke |
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A Computational Approach to Study the Energy Transduction Mechanism in the Na+/K+-ATPase
Ch. Weidemüller, K. Hauser |
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Improved Hydrogen Bond Potentials to Assess in Silico Protein Folding
M. G. Wolf, J. Vreede, P. G. Bolhuis, S. W. de Leeuw |
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Sequence Specific DNA Recognition by EcoRV
M. Zahran, P. Imhof, J. C. Smith |
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| Workshop Program
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| List of Participants
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