advertisement: compare things at compare-stuff.com!

Contents

• Contents
• List of Figures
• List of Tables
• Introduction
  • Protein structure and function
    • Primary structure
    • Secondary structure
    • Tertiary structure
    • Quaternary structure -- macromolecular assemblies
    • Soluble, fibrous and membrane proteins
    • Enzymes
    • Electron transfer proteins
    • Proteins in signalling and recognition
    • Mechanical proteins
    • Regulation and control of protein function
  • Protein structure classification
    • The dynamic programming alignment algorithm
    • Structural alignment
    • Classification schemes
  • Molecular interactions of proteins
    • Protein surfaces and binding
    • Molecular surfaces
    • Docking
  • Prediction of protein structure and function
    • Sequence methods
    • Fold recognition
    • Comparative modelling
    • Ab initio methods
    • CASP - Critical Assessment of Structure Prediction
  • Outline of thesis
• Antibody-antigen interactions
  • Introduction
  • Methods and Data
    • Antibody structures and sequences
    • Accessibility and burial
    • Canonical loops and structural alignment
    • Surface analysis
  • Results
    • Contact Analysis
    • Antibody surface topography
    • Predicting antigen contacts
  • Discussion
• Class and architecture prediction
  • Introduction
  • Class prediction
    • Overview of algorithm
    • Dataset size
    • Dataset completeness and class definitions
    • Pairwise similarity
    • Jack-knifing
    • Sequence length and noise
    • Multiple sequences
    • N-tuple composition
    • Prediction confidence
    • Helix/non-helix prediction
  • Secondary structural content prediction
  • Hierarchical class and architecture prediction
    • Distinction between mainly-$\alpha$ and mixed-$\alpha \beta$ classes
    • Prediction of mainly-$\beta$ architectures
    • Prediction of other architectures
  • Origins of sequence composition differences
    • Methods -- Analysis of sequence pattern usage
    • Secondary structural class
    • Mainly-$\beta$ architectures
  • Discussion
• Alignments of multiple sequence-derived property vectors
  • Introduction
    • Sequence properties and derived information
  • Methods and Data
    • Fold library and query sequences
    • Evaluation of fold recognition performance
    • Evaluation of alignment quality
    • Sequence alignment algorithm
  • Results
    • Baseline comparison -- Smith Waterman searches of the fold library
    • Alignments of hydrophobicity-related information
    • Sequence Conservation
    • Secondary structure predictions
  • Analysis and Discussion
    • Respectable fold recognition from sequence alone?
    • Length dependence and local alignments
    • The Fischer and Eisenberg benchmark
    • Significance estimates and null predictions
    • Alignment quality
    • Future developments of SIVA
• Self-organising maps of protein structure and sequence
  • Introduction
  • Self-organising maps - Overview
    and Methods
    • Implementation
    • Visualisation
  • Mapping of three-dimensional protein structure
    • Self-organising maps of two superfolds
    • Map discontinuities
    • Map dimensions
    • Fold essence
  • Mapping of structure and sequence properties
    • Sequence-derived hydropathy
    • Sequence conservation
    • Predicted secondary structure information
  • Alignment of structure-mapped sequence information
    • Methods -- fold recognition using mapped sequences
    • Results -- fold recognition using mapped sequences
    • Alignment quality for $\alpha \beta$ doubly wound folds
    • Gap penalties
  • Analysis and Discussion
    • Possible developments
• Concluding remarks
• Gathering multiple sequences for protein domains
  • Overview
  • Domain sequences
  • Database search
  • Multiple sequence alignments
  • Indel removal
  • Removal of redundant sequences (weeding)
• CATH descriptions
  • Architectures
  • Topologies
• Bibliography
• About this document ...