Inhalt

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  Introduction
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   Molecular Biology
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   Computational Biology
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  Biological Background: Proteins
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  Structural and Chemical Properties
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   Structure
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   Weak Forces
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   Protein Structure Data
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   Protein Function and -Interaction
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   Experimental Complex Determination
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   Interaction Data
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   Conformational Changes
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  Rotamer Flexibility
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   Rotamer Statistics
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   Energy Calculation
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   Computational Protein Docking
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  Existing approaches to Protein Docking
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   Energy Calculation including Solvation free Energy
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   Interactive Molecular Dynamics
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   Geometry based Protein-Protein Docking
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   Post-Docking Filters
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   Prediction of NMR Spectra
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   Incorporation of Flexibility into Docking Algorithms
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  Test and Training Data
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   Available Benchmark Data Sets
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  Automated Test Set Creation
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   Two-chain Complexes
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   Keyword based Classification Scheme
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   Combining the Test Sets
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   A Database Schema for Complexes and Unbound Test Cases
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   Creating Synthetic Complexes
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  System Design and -Components
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   System Architecture
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  Preprocessing Protein Data
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   The Pdb Server
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   Voxel and Feature Extraction
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   Segment Server
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   Docking Modules
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   Initial Docking
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   Elastic Docking and Scoring
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   Flexibility Calculations
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  Validation
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   Graphical Representation of Docking Results
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   Performance Indicators
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   Integrated Performance Indicator
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  Communication and Infrastructure
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   Database Integration
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   Network Streams
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  System Evaluation
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   Characterisation of the Test Set
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  Experiments and Results
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   Bound Docking
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   Characterisation of the Integrated Performance Indicator
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   Unbound Docking
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   Flexible Docking
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   Energy based Flexibility
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   Statistics based Flexibility
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   Memory and Runtime Requirements
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   Parallelisation Results
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  Determining the biologically active Contact Site
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   Crystal Packing
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   Scoring Monomer and Dimer Contact Areas
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   Discussion of Results
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  Conclusion
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   Summary
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  Outlook
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   Additional Post processing
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   User Interface for Navigation
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   1:N Protein Docking
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   Scheduling for Any-Time Evaluation
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   Test Sets
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   B. Curriculum Vitae
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   List of Figures
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   List of Tables
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   Bibliography