Preface
Ulrich H.E. Hansmann
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| Invited Talks |
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Cluster Distance Geometry and Protein Folding
G. M. Crippen |
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From Simulation to Therapy: A Systems Biology Approach to Oncogene Detection
A. Gosh, D. Pant, A. Kumar, R. Zou, D. Miller |
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Protein Aggregation and Unfolding Studied Using an All-Atom Model with a Simplified Energy Function
A. Irbäck, S. Mitternacht |
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Modeling Protein Structure, Dynamics and Thermodynamics with Reduced Representation of Conformational Space
A. Kolinski, D. Gront, S. Kmiecik, M. Kurcinski, D. Latek |
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A High-Speed Special-Purpose Computer for Molecular Dynamics
Simulations: MDGRAPE-3
T. Narumi, Y. Ohno, N. Futatsugi, N. Okimoto, A. Suenaga, R. Yanai, M. Taiji |
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The Two Aspects of the Protein Folding Problem
H.A. Scheraga, A. Liwo, St. Oldziej, C. Czaplewski, M. Khalili, J.A. Villa, D.R. Ripoll
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De novo all atom folding of helical proteins
A. Verma, S. Murthy, K. H. Lee, E. Starikov, W. Wenzel
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Dewetting in Nanoscale Hydrophobic Plates Collapse and Protein
Complex Folding
R. Zhou
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| Contributed Talks |
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Reduction to the Simplest -- The Complexity of Minimalistic Heteropolymer Models
M. Bachmann, W. Janke |
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Multiplexed-Replica Exchange Molecular Dynamics with the UNRES
Force-Field as an Effective Method for Exploring the Conformational
Energy Landscape of Proteins.
C. Czaplewski, S. Kalinowski, S. O{\l}dziej, A. Liwo, H. A. Scheraga |
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Single Amino Acid Contributions to Binding Affinity in Enzyme-Inhibitor Interactions: a Docking-Based Screening of BPTI-Beta Trypsin interaction
D. Dell'Orco, P. G. De Benedetti, F. Fanelli |
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Sub-type Specific Sites for SMAD Receptor Binding Identified by
Sequence Comparison Using "Sequence Harmony"
K. A. Feenstra, W. Pirovano, J. Heringa |
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High Throughput Method for Protein Structure Prediction
D. Gront, S. Kmiecik, A. Kolinski |
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From Microscopic Monte-Carlo Simulations to Macroscopic Solvation Models
M.Gruziel, W. R. Rudnicki, B. Lesyng |
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A Very General Solvation Model for BioMolecular Simulation
S. Höfinger |
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Prediction of Domain Interactions in C. elegans
F. Morcos, M. Boxem, N. Klitgord, M. Vidal, J. A. Izaguirre |
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Adsorption Phenomena at Organic-Inorganic Interfaces
M. Bachmann, W. Janke |
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Modelling protein-DNA interactions in chromatin
G. La Penna, S. Furlan, L. Arcesi, A. Perico |
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Molecular Dynamics Study of Amyloid Formation of Two
Abl-SH3 Domain Peptides
I. Liepina, S. Ventura, C. Czaplewski, A. Liwo |
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Optimization of the United-Residue UNRES Force Field for Langevin
Dynamics Simulations
A. Liwo, M. Khalili, C. Czaplewski, S. Kalinowski, S. Oldziej, H. A. Scheraga |
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Simple Physics-Based Analytical Formulas for the Potentials of Mean
Force for the Interaction for Amino-Acid Side Chains in Water. Tests with Simple
Spherical Systems
M. Makowski, A. Liwo, K. Maksimiak, J. Makowska, L. Chmurzynski, H. A. Scheraga |
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The Role of Flexible Stem Geometries in Protein Loop Structure Prediction
M. Mönnigmann, C. A. Floudas |
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Modeling of Water Explicitly in the Replica-Exchange Simulation Method for Protein Folding
Y. Mu, Y. Yang |
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Molecular Transport Through Channels and Pores
W. Nadler, W. R. Bauer |
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Integrating Structural and Kinetic Enzymatic Information in Systems Biology
M. Stein, R. R. Gabdoulline, R. C. Wade |
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Secondary Structure of Compstatin Analogues: Insights from Molecular
Dynamics Simulations in Explicit Water
Ph. Tamamis, G. Archontis |
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Using Simple Fluid Wetting as a Model for Cell Spreading
M. Reuter, C. Taylor |
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| Posters |
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Parallel Cost-Sensitive Support Vector Machine Software for Classification
T. Eitrich, B. Lang |
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A Study on the Structure and Dynamics of Spin Labeled Proteins by MD Simulations and EPR Spectroscopy
P. Gajula, I. V. Borovykh, Ch. Beier, P. Gast, M. Huber, H.-J. Steinhoff |
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An Improved Evolutionary Strategy for Protein Structure Prediction
S. M. Gopal, K. H. Lee, W. Wenzel |
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Ab initio Simulations of Cu Binding Sites in the N-Terminal Region of PrP
S. Furlan, F. Guerrieri, G. La Penna, S. Morante, G.C. Rossi |
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Cross-Check Methods in Protein Simulations
Ch. Junghans, U.H.E. Hansmann |
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The Influence of Molecular Surface Composition on the Outcome
of Poisson Boltzmann Calculations Performed to Obtain Solvation
Free Energies
P. Kar, Y. Wei, U.H.E. Hansmann, S. Höfinger |
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Generalized Born and Nonpolar Models in Solvation Free Energies.
P. Kmiec, J. Kalinowski, B. Lesyng |
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Determination of Short-Range Potentials for Physics-Based Protein-Structure Prediction
U. Kozlowska, K. Wachucik, A. Liwo, H. A. Scheraga |
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Large Scale Molecular Dynamics Simulations for the Derivation of Solvation Free Energies of Strongly Hydrophobic Molecules
R. Mahajan, D. Kranzlmüller, J. Volkert, S. Höfinger |
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Simulation of Thick Polymers
T. Neuhaus, O. Zimmerman, U.H.E. Hansmann |
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Symplectic Algorithms of Molecular Dynamics. An Application to the United-Residue Model.
F. Rakowski, P. Grochowski, B. Lesyng, A. Liwo, H. A. Scheraga |
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A Fast Wavelet Based Evaluation of Coulomb Potentials in Molecular Systems
G. Sutmann, S. Wädow |
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A Highly Accurate and Optimal Method to Calculate Long Range Interactions
M. Bolten, G. Sutmann |
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Evolutionary Analysis in Pathogenesis-Related Proteins
N. M. Scherer, C. E. Thompson, L. B. Freitas, S. L. Bonatto, F. M. Salzano |
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A Parameterized Procedure for Consensus Sequences - Validation of the Method
S. Walkowiak, B. Lesyng |
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Prediction of Parallel and Antiparallel Beta Sheets Based on Sequence Profiles Using Support Vector Machines
L. Wang, O. Zimmerman, U.H.E. Hansmann |
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Side-Chain Ordering in PolyGlutamic Acid
Y. Wei, W. Nadler, U. H. E. Hansmann |
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