Inhalt

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   Contents
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   Introduction
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   Principles of Modern Protein Analysis
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   The Central Dogma of Molecular Biology
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  Proteins: The Fundamentals of Life
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   Biochemical Composition
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   Biological Relevancy
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  Protein Relationships
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   Protein Families
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   Exemplary Hierarchical Classification
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  Protein Analysis
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   The Drug Discovery Process
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   Protein Sequence Analysis
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   Summary
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   Computational Protein Sequence Analysis
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   Pairwise Sequence Alignment
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   Principles of Sequence Alignment
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   Heuristic Approximations
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   Analysis of Sequence Families
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   Profile Analysis
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   Profile Hidden Markov Models
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   Further Probabilistic Modeling Approaches
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   Signal Processing based Sequence Comparison
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   Alternative Representations of Protein Sequences
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   Signal Processing Methods for Classification
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   Summary
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   Concepts for Improved HMM Based Sequence Analysis
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  Assessment of Current Methodologies' Capabilities
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   Task: Homology Detection at the Superfamily Level
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   Capabilities of State-of-the-Art Approaches
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   Improving the Quality of HMM Based Sequence Analysis
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   Semi-Continuous Feature Based Modeling
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   Model Architectures with Reduced Complexity
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   Accelerating the Model Evaluation
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   Summary
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   Advanced Probabilistic Models for Protein Families
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  Feature Extraction from Protein Sequences
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   Rich Signal-Like Protein Sequence Representation
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   Feature Extraction by Abstraction
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   Robust Feature Based Profile HMMs and Remote Homology Detection
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   Feature Space Representation
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   General Semi-Continuous Profile HMMs
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   Specialization by Adaptation
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   Explicit Background Model
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   Protein Family HMMs with Reduced Complexity
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   Beyond Profile HMMs
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   Protein Family Modeling using Sub-Protein Units (SPUs)
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   Accelerating the Model Evaluation by Pruning Techniques
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   State-Space Pruning
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   Combined Model Evaluation
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   Optimization of Mixture Density Evaluation
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   Summary
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  Evaluation
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   Methodology and Datasets
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   Effectiveness of Semi-Continuous Feature Based Profile HMMs
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  Advanced Stochastic Protein Family Models for Small Training Sets
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   Effectiveness of Sub-Protein Unit based Models
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   Effectiveness of Bounded Left-Right Models
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   Acceleration of Protein Family HMM Evaluation
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   Effectiveness of State-Space Pruning
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   Effectiveness of Accelerated Mixture Density Evaluation
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   Combined Evaluation of Advanced Stochastic Modeling Techniques
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   Summary
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   Conclusion
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  Wavelets
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   Fourier Analysis
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   Continuous Wavelet Transformation
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   Discrete Wavelet Transformation
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   Principal Components Analysis (PCA)
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   Amino Acid Indices
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   Detailed Evaluation Results
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   Bibliography