Patterns in Protein Sequence and Structure

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William R. Taylor
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- 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 Ten
The contents of this volume derive loosely from an EMBO worksh9P held at EMBL (Heidelberg) towards the end of 1989. The topic of Patterns in Protein Sequence and Structure attracted a wide range of participants, from biochemists to computer scientists, and that diversity has, to some extent, remained in the contributions to this volume. The problems of interpreting biological sequence data are to an increasing extent forcing molecular biologists to learn the language of computers, including at times, even the abstruse language of the computer scientists themselves. While, on their side, the computer scientists have discovered a veritable honey-pot of real data on which to test their algorithms. This enforced meeting of two otherwise alien fields has resulted in some difficulties in communication and it was an aim of the EMBO workshop to help resolve these. By the end, most biologists at the meeting had, at least, heard the terms Dynamic Programming and Regular Expression while for their part the computer programmers began to realise that protein sequences might be more than simple Markov chains in a 20-letter alphabet. Thanks to the modern facilities at EMBL, the three day meeting was video-taped and from this a transcript was taken and offered to the speakers as the basis for a contribution to this volume.