Patterns in Protein Sequence and Structure

- Patterns, Predictions and Problems.- The Ultimate Rationale.- Protein Structure Prediction.- Motifs and Modelling.- Computational Techniques.- Current Problems in Pattern Matching.- Conclusions.- A Brief Review of Protein Sequence Pattern Matching.- Pattern Matching Methods in the Prediction of Protein Structure and Function.- Consensus Methods.- Regular Expressions.- Specific Structural Patterns.- Recent Work.- Multiple Sequence Alignment and Flexible Pattern Matching.- Background to Automatic Protein Sequence Alignment.- Multiple Sequence Alignment.- Flexible Pattern Matching.- Discussion.- SCRUTINEER: a Program to Explore and Evaluate Protein Sequence Patterns in Databases.- Description of the Program.- New Features of SCRUTINEER.- A Sample Session.- Planned Enhancements.- Pattern Exploration and Evaluation.- Examples of Motif Development.- Current Issues.- Availability of SCRUTINEER.- Patterns and Specificity - Nucleotide Binding Proteins and Helicases.- Conservation Patterns.- Structural Sources of Patterns.- Nucleotide Binding Patterns.- Nucleotide Binding Pattern Specificity.- Helicases.- Conclusions.- Discussion.- The Helix-Turn-Helix Motif and the Cro Repressor.- Comparative Structural Studies.- Sequence Analysis and Motif Matching.- Predicted Motifs.- New Structural Studies.- Discussion.- Assignment of ?-Helices in Multiply Aligned Protein Sequences - Applications to DNA Binding Motifs.- Usage of Hydrophobic Information in Helical Prediction.- Examples of Helical Prediction in DNA-Binding Domains.- Leucine Zipper.- Zinc Finger.- The Myb DNA-Binding Domain.- Helix-Loop-Helix Domain.- Rules for Detection of Helices in Multiply Aligned Sequences.- Assignment of ?-Strands.- Automation.- An Expert System for Secondary Structure Prediction.- Four Helix Bundles.- Secondary Structure Prediction.- Discussion.- Patterns in Secondary Structure Packing - a Database for Prediction.- Topology, Packing and Geometry.- Parameter Selection.- Applications and Continuing Work.- Secondary and Supersecondary Motifs in Protein Structures.- Protein Structure Database Development.- Protein Structure Hierarchy.- Analysis of ?-Turns.- Supersecondary Structures.- ?-Hairpin Classification.- Modelling ?-Hairpins.- ?-Arches.- Other Supersecondary Structures.- Conclusion.- Discussion.- A Review of Methods for Protein Structure Comparison.- Methods Based on Comparison of Inter-Residue Distances.- Distance Plots.- Method of Padlan and Davies.- Sippl's Method.- Methods Comparing the Geometry of Fragments Along the Polypeptide Chain.- Rackovsky's Method.- Levine's Method.- Karpen Variation.- Method of Nussinov and Wolfson.- Methods Which Superpose Protein Structures or Fragments of Structure.- Method of Remington and Matthews.- Methods Based On the Geometry of Secondary Structures.- Murthy's Methods.- Graph Method of Mitchell et al.- Methods Incorporating Dynamic Programming Techniques.- Method of Zuker and Somorjai.- S?li and Blundell's Method.- Method of Taylor and Orengo.- Conclusions.- Patterns of Sequence and 3-D Structure Variation in Families of Homologous Proteins: Lessons for Tertiary Templates and Comparative Modelling.- X-Ray Analyses of Families of Proteins.- Rules Expressed as Environment-Specific Substitution Tables.- Rules for Generating Tertiary Templates.- Rules for Modelling Three-Dimensional Structure.- Discussion.- Modelling From Remote Sequence Similarity - Enveloped Virus Capsid Structure Modelled on the Non-Enveloped Capsid.- Virus Structure.- 3D Electron Microcopy of Enveloped Capsids.- Comparative Sequence Analysis.- Structural Model and Experimental Tests.- Conclusions.- Discussion.- Structural Motifs of the Extracellular Matrix Proteins Laminin and Tenascin.- Structural Organization of Laminin and Tenascin.- Sequence Arrangement of Laminin and Tenascin.- Sequence Motifs of Laminin and Tenascin.- Amino-Terminal Domains.- Cysteine-Rich Domains.- Heptad Repeats (?-Helical Coiled-Coils).- Fibronectin Type III Repeats of Tenascin.- Homology of Sex Hormone Binding Globulin to C-Terminus of Laminin A-Chain.- Fibrinogen Homology to C-Terminus of Tenascin.- "Molecular Modelling" by Motif Analysis and Electron Microscopy.- A Sequence Motif in the Transmembrane Region of Tyrosine Kinase Growth Factor Receptors.- Neu Dimerisation.- Sequence Motif.- Conclusion.- Discussion.