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URN: urn:nbn:de:0001-00422, 13 Mb PDF free download

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A fundamental book on Computational Biophysics and Systems Biology theory. From the contents: "Preface Ulrich H. E. Hansmann Invited Talks: The Slip-Length Effects in Molecular Dynamics of Bead-Like Models of Proteins P. Szymczak, M. Cieplak PDF Advances in De Novo Protein Design Ch. A. Floudas, H. K. Fung, M. S. Taylor PDF Chromatin Dynamics in silicio J. Langowski PDF Causality and Correlation Analyses of Molecular Dynamics Simulation Data A. Gorecki, J. Trylska, B. Lesyng PDF Mesoscopic Dynamics with the UNRES Force Field - a Tool for Studying the Kinetics and Thermodynamics of Protein Folding A. Liwo, C. Czaplewski, S. Odziej, M. Chinchio, A. V. Rojas, M. Khalili, M. Makowski, S. Kalinowski, U. Kozlowska, R. K. Murarka, H. A. Scheraga PDF Mixed QM/MM Calculations in Biological Systems G. M. Seabra, J. Torras, R. C. Walker, A. Roitberg PDF Evolution of Experimental and Theoretical Determinations of Protein Structure and Protein Folding Pathways H. A. Scheraga, A. Liwo, C. Czaplewski, S. Odziej PDF The E-Cell Project and Challenges in Computational Systems Biology K. Takahashi PDF Stretching RNA Hairpins C. Hyeon, D. Thirumalai PDF Simulation of Linker Histone-Chromatin Interactions G. V. Pachov, R. R. Gabdoulline, R. C. Wade PDF Contributed Talks and Posters Conformational Study of Amyloid Beta (ABeta) Peptide P. Anand, F. S. Nandel PDF Global Persistence Exponent of the Helix-Coil Transition in Polypeptides E. Arashiro, J. R. Drugowich de Feli­cio, U. H. E. Hansmann PDF Coarse-Grained Lattice Model for Molecular Recognition H. Behringer, A. Degenhard, F. Schmid PDF Residual Entropy of Ice I from Multicanonical Simulations B. A. Berg PDF REMD Simulations of A16-22 Peptide Aggregation in Explicit Solvent R. R. Burri, D. Paschek, A. Geiger PDF A Molecular Dynamic Study of the Basic Fibroblast Growth Factor - Fibroblast Growth Factor Receptor Complex L. Degrave, G. H. Brancaleoni PDF Dimensionality Reduction Techniques for Protein Folding Trajectories T. Eitrich, S. Mohanty, X. Xiao, U. H. E. Hansmann PDF Chemical Space of Auxins, their Multi-Phenomenology and Multiple Protein Interaction N. Ferro, P. Bultinck, Th. Bredow, Th. Reinard PDF Crystal Water Molecules and Solvation Effects on Protein-Ligand Docking B. Fischer, W. Wenzel PDF Semiautomatic Workflow for Fold Recognition - Results from the CASP 2006 Competition F. Fredel, J. Meinke, S. Mohanty, O. Zimmermann, U. H. E. Hansmann PDF Interaction of Biological Matter with Nanomaterials: A First-Principles Approach S. Gowtham, R. H. Scheicher, R. Ahuja, R. Pandey PDF Computational Reconstruction of Macromolecular Assemblies A. Griewel, M. Rarey PDF Verification of Protein-Protein Interactions by Use of Docking Techniques F. Fink, R. Merkl, W. Gronwald PDF Boundary Element Method (BEM) with Parametric Surfaces S. Grudinin, A. Baumgaertner PDF Parameterization of the Potential Energy Surface of the Double Proton Transfer in Porphyrins M. Hallay-Suszek, P. Grochowski, B. Lesyng PDF 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 PDF Simulation of Small Peptide Using Combined Wang-Landau-Transition Matrix Monte Carlo Algorithm Sh. Hayryan, R. Ghulghazaryan, N. Poklar Ulrih, V. Lurin Qerbec, C.-K.Hu PDF Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity M. Held, E. Meerbach, St. Hinderlich, W. Reutter, Ch. Schatte PDF Photosensory Proteins as a Tool in Synthetic Biology: Bridging Computational Biophysics and Systems Biology J. Hendriks, M. Avila Perez, F. Bruggeman, K. J. Hellingwerf PDF Comparing Semi-Empirical versus Classic Charge Assignments in BioMolecules and their Effect on Electrostatic Potentials P. Kar, M. Seel, U. H. E. Hansmann, S. Hafinger PDF Role of Filopodia in Adhesion Formation During Migration of Epithelial Cells B. Borm, S. Born, R. Merkel, B. Hoffmann PDF Study of Protein Structural Descriptors: Towards Similarity and Classification P. Jain, J. D. Hirst PDF Phase Separation in Peptide Aggregation Processes - Multicanonical Study of a Mesoscopic Model Ch. Junghans, M. Bachmann, W. Janke PDF Algorithmic Refinements to an Enhanced Poisson-Boltzmann Approach Used in BioMolecular Simulation P. Kar, M. Seel, U. H. E. Hansmann, S. Hafinger PDF Aggregation of the Amyloid-a-beta Protein: Monte Carlo Optimization Study S. M. Gopal, K. V. Klenin, W. Wenzel PDF Analysis and Optimization of the Flex-Screen Docking Approach Using DUD Benchmarking Database D. Kokh, B. Fischer, W. Wenzel PDF Folding and Structure Prediction of Proteins Containing Disulfide Bridges I. Kondov, A. Verma, W. Wenzel PDF DNA Packaging and Electrostatic Interactions N. Korolev, L. Nordenskild PDF Water Percolation Governs Polymorphic Transition and Conductivity of DNA I. Brovchenko, A. Krukau, A. Oleinikova, A. Mazur PDF Molecular Dynamics in Excited States: Landau-Zener Model of Nitric Oxide Geminate Recombination to Nitrile Hydratase K. Kubiak, W. Nowak PDF Exploring Conformational Space and Dynamics of RNA Hairpins by MD Simulations: Structure-Function Correlation of HIV-1 Genome Regulatory Elements K. Kulinska, T. Kulinski PDF Anisotropic Internucleosome Interactions and Geometrical Constraints Favour the Two-Start Helical Structure of Chromatin G. La Penna, G. Cinacchi, A. Perico PDF Mechanism of Fibril Formation of A-beta-16-22 Peptides M. S. Li, P. H. Nguyen, D. Thirumalai PDF Multiple Beta-Sheet Molecular Dynamics of Two Abl-SH3 Domain Peptides I. Liepina, S. Ventura, C. Czaplewski, A. Liwo PDF Parallelization of ECEPP/3 in SMMP J. H. Meinke, U. H. E. Hansmann PDF 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 PDF Folding and Aggregation of Proteins with Monte Carlo Simulations S. Mohanty, U. H. E. Hansmann PDF Channel Transport and Molecular Motors without Brownian Ratchets W. Nadler, W. R. Bauer PDF Aggregate Size and Shape Distributions in Amyloid-a-beta Peptide Solutions L. Nagel-Steger, B. Demeler, D. Willbold PDF PSO@Autodock : A Novel Bio-Algorithm-Based Fast Flexible Docking Tool for Virtual Screening V. Namasivayam, R. Gunther PDF Efficient Parallel Tempering with Multiple Gaussian Modified Ensembles M. Magiera, T. Neuhaus, U. H. E. Hansmann PDF A Network-Based Approach to Biomolecular Dynamics F. Noé, J. C. Smith, Ch. Schatte PDF Steered Molecular Dynamics as a Virtual Atomic Force Microscope W. Nowak, S. Wasilewski, L. Peplowski PDF 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 PDF The Locally Enhanced Sampling Study of Large Ligands Diffusion inside Enzyme. Acrylonitrile and Acrylamide Journey in Nitrile Hydratase L. Peplowski, K. Kubiak, W. Nowak PDF Receptor Specific Forcefield: Improving Classical Forcefields with Quantum Mechanical Calculations H. E. Perez Sanchez, B. Fischer, H. Merlitz, K. Fukuzawa, W. Wenzel PDF Folding of Two Helical Peptide with Free Energy Methods and Molecular Dynamics A. Quintilla, W. Wenzel PDF Multiscale Simulation of Protein Cluster Dynamics - the Encounter Complex J. Schluttig, D. Alamanova, V. Helms, U. Schwarz PDF Aggregation of Fragments of the Islet Amyloid Polypeptide as a Phase Transition: A Cluster Analysis G. Singh, I. Brovchenko, A. Oleinikova, R. Winter PDF A Load Balanced Force-Domain Decomposition Algorithm for Parallel Molecular Dynamics Simulations G. Sutmann, F. Janoschek PDF Forcefield Validation with the Rosetta Protein Decoy Set A. Verma, W. Wenzel PDF Knots in Macromolecular Systems: Concepts and Challenges P. Virnau PDF Steered Classical and Quantum Path-Integral Molecular Dynamics Simulations of Strongly Coupled Protons Motions in Porphycene A. Walewski, P. Baa, B. Lesyng PDF Side-Chain Ordering in Homopolymers Y. Wei, W. Nadler, U. H. E. Hansmann PDF Dihedral Angle Patterns in Coil Regions of Protein Structures O. Zimmermann, U. H. E. Hansmann PDF Workshop Program."

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Open access: http://www.fz-juelich.de/nic-series/volume36/volume36.html M.Kamps@fz-juelich.de, 08-Aug-2007 URL:

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