Ebook: Patterns in Protein Sequence and Structure

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.

---

---

Content:
Front Matter....Pages I-XII
Introduction — Patterns, Predictions and Problems....Pages 1-9
A Brief Review of Protein Sequence Pattern Matching....Pages 11-28
Multiple Sequence Alignment and Flexible Pattern Matching....Pages 29-52
Discussion....Pages 53-56
SCRUTINEER: a Program to Explore and Evaluate Protein Sequence Patterns in Databases....Pages 57-68
Patterns and Specificity — Nucleotide Binding Proteins and Helicases....Pages 69-83
Discussion....Pages 84-84
The Helix-Turn-Helix Motif and the Cro Repressor....Pages 85-95
Discussion....Pages 96-98
Assignment of ?-Helices in Multiply Aligned Protein Sequences — Applications to DNA Binding Motifs....Pages 99-110
An Expert System for Secondary Structure Prediction....Pages 111-122
Discussion....Pages 123-125
Patterns in Secondary Structure Packing — a Database for Prediction....Pages 127-140
Secondary and Supersecondary Motifs in Protein Structures....Pages 141-155
Discussion....Pages 156-158
A Review of Methods for Protein Structure Comparison....Pages 159-188
Patterns of Sequence and 3-D Structure Variation in Families of Homologous Proteins: Lessons for Tertiary Templates and Comparative Modelling....Pages 189-204
Discussion....Pages 205-205
Modelling From Remote Sequence Similarity — Enveloped Virus Capsid Structure Modelled on the Non-Enveloped Capsid....Pages 207-225
Discussion....Pages 226-227
Structural Motifs of the Extracellular Matrix Proteins Laminin and Tenascin....Pages 229-254
A Sequence Motif in the Transmembrane Region of Tyrosine Kinase Growth Factor Receptors....Pages 255-261
Discussion....Pages 262-262

---

Content:
Front Matter....Pages I-XII
Introduction — Patterns, Predictions and Problems....Pages 1-9
A Brief Review of Protein Sequence Pattern Matching....Pages 11-28
Multiple Sequence Alignment and Flexible Pattern Matching....Pages 29-52
Discussion....Pages 53-56
SCRUTINEER: a Program to Explore and Evaluate Protein Sequence Patterns in Databases....Pages 57-68
Patterns and Specificity — Nucleotide Binding Proteins and Helicases....Pages 69-83
Discussion....Pages 84-84
The Helix-Turn-Helix Motif and the Cro Repressor....Pages 85-95
Discussion....Pages 96-98
Assignment of ?-Helices in Multiply Aligned Protein Sequences — Applications to DNA Binding Motifs....Pages 99-110
An Expert System for Secondary Structure Prediction....Pages 111-122
Discussion....Pages 123-125
Patterns in Secondary Structure Packing — a Database for Prediction....Pages 127-140
Secondary and Supersecondary Motifs in Protein Structures....Pages 141-155
Discussion....Pages 156-158
A Review of Methods for Protein Structure Comparison....Pages 159-188
Patterns of Sequence and 3-D Structure Variation in Families of Homologous Proteins: Lessons for Tertiary Templates and Comparative Modelling....Pages 189-204
Discussion....Pages 205-205
Modelling From Remote Sequence Similarity — Enveloped Virus Capsid Structure Modelled on the Non-Enveloped Capsid....Pages 207-225
Discussion....Pages 226-227
Structural Motifs of the Extracellular Matrix Proteins Laminin and Tenascin....Pages 229-254
A Sequence Motif in the Transmembrane Region of Tyrosine Kinase Growth Factor Receptors....Pages 255-261
Discussion....Pages 262-262
....