Preface
Ulrich H. E. Hansmann
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Invited Talks |
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The Slip-Length Effects in Molecular Dynamics of Bead-Like Models of Proteins
P. Szymczak, M. Cieplak |
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Advances in De Novo Protein Design
Ch. A. Floudas, H. K. Fung, M. S. Taylor
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Chromatin Dynamics in silicio
J. Langowski
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Causality and Correlation Analyses of Molecular Dynamics Simulation Data
A. Gorecki, J. Trylska, B. Lesyng
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Mesoscopic Dynamics with the UNRES Force Field - a Tool for Studying
the Kinetics and Thermodynamics of Protein Folding
A. Liwo, C. Czaplewski, S. Ołdziej, M. Chinchio, A. V. Rojas,
M. Khalili, M. Makowski, S. Kalinowski, U. Kozłowska, R. K. Murarka, H. A. Scheraga
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Mixed QM/MM Calculations in Biological Systems
G. M. Seabra, J. Torras, R. C. Walker, A. Roitberg
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Evolution of Experimental and Theoretical Determinations of Protein Structure and Protein Folding Pathways
H. A. Scheraga, A. Liwo, C. Czaplewski, S. Ołdziej
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The E-Cell Project and Challenges in Computational Systems Biology
K. Takahashi
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Stretching RNA Hairpins
C. Hyeon, D. Thirumalai
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Simulation of Linker Histone-Chromatin Interactions
G. V. Pachov, R. R. Gabdoulline, R. C. Wade
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Contributed Talks and Posters |
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Conformational Study of Amyloid Beta (ABeta) Peptide
P. Anand, F. S. Nandel
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Global Persistence Exponent of the Helix-Coil Transition in Polypeptides
E. Arashiro, J. R. Drugowich de Felício, U. H. E. Hansmann
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Coarse-Grained Lattice Model for Molecular Recognition
H. Behringer, A. Degenhard, F. Schmid
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Residual Entropy of Ice I from Multicanonical Simulations
B. A. Berg
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REMD Simulations of Aβ16-22 Peptide Aggregation in Explicit Solvent
R. R. Burri, D. Paschek, A. Geiger
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A Molecular Dynamic Study of the Basic Fibroblast
Growth Factor - Fibroblast Growth Factor Receptor Complex
L. Degrève, G. H. Brancaleoni
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Dimensionality Reduction Techniques for Protein Folding Trajectories
T. Eitrich, S. Mohanty, X. Xiao, U. H. E. Hansmann
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Chemical Space of Auxins, their Multi-Phenomenology and Multiple Protein Interaction
N. Ferro, P. Bultinck, Th. Bredow, Th. Reinard
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Crystal Water Molecules and Solvation Effects on Protein-Ligand Docking
B. Fischer, W. Wenzel
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Semiautomatic Workflow for Fold Recognition - Results from the CASP 2006 Competition
F. Fredel, J. Meinke, S. Mohanty, O. Zimmermann,
U. H. E. Hansmann
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Interaction of Biological Matter with Nanomaterials:
A First-Principles Approach
S. Gowtham, R. H. Scheicher, R. Ahuja, R. Pandey
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Computational Reconstruction of Macromolecular Assemblies
A. Griewel, M. Rarey
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Verification of Protein-Protein Interactions by Use of Docking Techniques
F. Fink, R. Merkl, W. Gronwald
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Boundary Element Method (BEM) with Parametric Surfaces
S. Grudinin, A. Baumgaertner
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Parameterization of the Potential Energy Surface of the Double Proton Transfer in Porphyrins
M. Hallay-Suszek, P. Grochowski, B. Lesyng
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A Statistical Approach to Deriving and Analyzing a Propensity Scale for Predicting Exposed Transmembrane Beta Barrel Residues from Protein Sequence
S. Hayat, Y. Park, V. Helms
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Simulation of Small Peptide Using Combined Wang-Landau-Transition Matrix Monte Carlo Algorithm
Sh. Hayryan, R. Ghulghazaryan, N. Poklar Ulrih, V. Čurin Šerbec, C.-K.Hu
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Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity
M. Held, E. Meerbach, St. Hinderlich, W. Reutter, Ch. Schütte
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Photosensory Proteins as a Tool in Synthetic Biology: Bridging Computational Biophysics and Systems Biology
J. Hendriks, M. Avila Perez, F. Bruggeman, K. J. Hellingwerf
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Comparing Semi-Empirical versus Classic Charge Assignments in BioMolecules and their Effect on Electrostatic Potentials
P. Kar, M. Seel, U. H. E. Hansmann, S. Höfinger
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Role of Filopodia in Adhesion Formation During Migration of Epithelial Cells
B. Borm, S. Born, R. Merkel, B. Hoffmann
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Study of Protein Structural Descriptors: Towards Similarity and Classification
P. Jain, J. D. Hirst
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Phase Separation in Peptide Aggregation Processes - Multicanonical Study of a Mesoscopic Model
Ch. Junghans, M. Bachmann, W. Janke
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Algorithmic Refinements to an Enhanced Poisson-Boltzmann Approach Used in BioMolecular Simulation
P. Kar, M. Seel, U. H. E. Hansmann, S. Höfinger
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Aggregation of the Amyloid-β Protein: Monte Carlo Optimization Study
S. M. Gopal, K. V. Klenin, W. Wenzel
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Analysis and Optimization of the Flex-Screen Docking Approach Using DUD Benchmarking Database
D. Kokh, B. Fischer, W. Wenzel
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Folding and Structure Prediction of Proteins Containing Disulfide Bridges
I. Kondov, A. Verma, W. Wenzel
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DNA Packaging and Electrostatic Interactions
N. Korolev, L. Nordenskiöld
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Water Percolation Governs Polymorphic Transition and Conductivity of DNA
I. Brovchenko, A. Krukau, A. Oleinikova, A. Mazur
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Molecular Dynamics in Excited States: Landau-Zener Model of Nitric Oxide Geminate Recombination to Nitrile Hydratase
K. Kubiak, W. Nowak
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Exploring Conformational Space and Dynamics of RNA Hairpins by MD
Simulations: Structure-Function Correlation of HIV-1 Genome Regulatory
Elements
K. Kulinska, T. Kulinski
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Anisotropic Internucleosome Interactions and
Geometrical Constraints Favour
the Two-Start Helical Structure of Chromatin
G. La Penna, G. Cinacchi, A. Perico
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Mechanism of Fibril Formation of Aβ16-22 Peptides
M. S. Li, P. H. Nguyen, D. Thirumalai
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Multiple Beta-Sheet Molecular Dynamics of Two Abl-SH3 Domain Peptides
I. Liepina, S. Ventura, C. Czaplewski, A. Liwo
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Parallelization of ECEPP/3 in SMMP
J. H. Meinke, U. H. E. Hansmann
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The Role of Metals in Misfolding and Aggregation Processes: X-ray Spectroscopy and Numerical Simulations
V. Minicozzi, S. Morante, G.C. Rossi, F. Stellato, K. Jansen
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Folding and Aggregation of Proteins with Monte Carlo Simulations
S. Mohanty, U. H. E. Hansmann
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Channel Transport and Molecular Motors without Brownian Ratchets
W. Nadler, W. R. Bauer
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Aggregate Size and Shape Distributions in Amyloid-β Peptide Solutions
L. Nagel-Steger, B. Demeler, D. Willbold
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PSO@Autodock : A Novel Bio-Algorithm-Based Fast Flexible Docking Tool for Virtual Screening
V. Namasivayam, R. Günther
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Efficient Parallel Tempering with Multiple Gaussian Modified Ensembles
M. Magiera, T. Neuhaus, U. H. E. Hansmann
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A Network-Based Approach to Biomolecular Dynamics
F. Noé, J. C. Smith, Ch. Schütte
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Steered Molecular Dynamics as a Virtual Atomic Force Microscope
W. Nowak, S. Wasilewski, L. Peplowski
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The Zinc-Finger Motif of T.thermophilus Ribosomal Protein S14 and the Functionality
of E.coli Ribosomes
G. Papadopoulos, M. A. Xaplanteri, F. Leontiadou,
Th. Choli-Papadopoulou, D. L. Kalpaxis
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The Locally Enhanced Sampling Study of Large Ligands Diffusion inside Enzyme. Acrylonitrile and Acrylamide Journey in Nitrile Hydratase
L. Peplowski, K. Kubiak, W. Nowak
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Receptor Specific Forcefield: Improving Classical Forcefields with Quantum Mechanical Calculations
H. E. Perez Sanchez, B. Fischer, H. Merlitz, K. Fukuzawa,
W. Wenzel
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Folding of Two Helical Peptide with Free Energy Methods and Molecular Dynamics
A. Quintilla, W. Wenzel
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Multiscale Simulation of Protein Cluster Dynamics - the Encounter Complex
J. Schluttig, D. Alamanova, V. Helms, U. Schwarz
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Aggregation of Fragments of the Islet Amyloid Polypeptide as a Phase Transition: A Cluster Analysis
G. Singh, I. Brovchenko, A. Oleinikova, R. Winter
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A Load Balanced Force-Domain Decomposition
Algorithm for Parallel Molecular Dynamics Simulations
G. Sutmann, F. Janoschek
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Forcefield Validation with the Rosetta Protein Decoy Set
A. Verma, W. Wenzel
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Knots in Macromolecular Systems: Concepts and Challenges
P. Virnau
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Steered Classical and Quantum Path-Integral Molecular Dynamics Simulations of Strongly Coupled Protons Motions in Porphycene
Ł. Walewski, P. Bała, B. Lesyng
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Side-Chain Ordering in Homopolymers
Y. Wei, W. Nadler, U. H. E. Hansmann
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Dihedral Angle Patterns in Coil Regions of Protein Structures
O. Zimmermann, U. H. E. Hansmann
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| Workshop Program
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| List of Participants
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