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Ruth V. Spriggs. Identification of ß-sheet motifs in three-dimensional protein structures, using a subgraph isomorphism algorithm: an update of a 1992 study.

Contents

Abstract

Acknowledgements

Introduction

Background
The Current Study
Overview of Report

Proteins

Protein Structure

Primary Structure
Secondary Structure
Supersecondary Motifs
Tertiary Structure
Quaternary Structure

How Protein Structure is Determined

X-Ray Crystallography
Nuclear Magnetic Resonance Spectroscopy

The Prediction of Protein Structure from Sequence

Empirical Methods
Theoretical Methods
Secondary Structure Prediction
Tertiary Structure Prediction

Protein Structure Evolution

The Function of Proteins

Literature Review

Searching Chemical Structure Databases

Two-Dimensional Chemical Structures
Three-Dimensional Chemical Structures

Searching Three-Dimensional Protein Structure Databases

Substructure Searching
Similarity Searching
Examples of the Use of 3D Protein Searching Methods

Methods

Overview

The Protein Data Bank and PDB_SELECT

The Search

BETPAT
POSSUM
Search Output

Analysis of Results

Data Preparation

Factors Which May Affect the Validity of Results

Occurrence vs. Incidence
Split Strands
ß-Barrels
Search Order

Analysis

Observations
Statistical Analysis

Discussion and Conclusions

Results of the Current (1999) Study

Comparison to 1992 Study

Methods
Results

Conclusions and Discussion

Suggestions for Improvements to the Current Study

Suggestions for Future Study

Bibliography

Reference List of Internet Pages

Appendices

Appendix A: Programs

a) four.c
b) rvs3c.c
c) rvs4c.c
d) rvs7c.c
e) 15aga.c
f) 15tif.c
g) 15mobi.c
h) larg5.c

Appendix B: Examples of Raw Data Files

a) 6str.log
b) st15.lp
c) la15.lp

Appendix C: Tables

Table 1) The Percentage of Possible Motifs Retrieved in 1999 and 1992
Table 2) The Frequency of Incidence of Motifs with each Number of Strands
Table 3) The Most Frequently Retrieved Motif for each Number of Strands
Table 4) Data for Three, Four, and Five Stranded Sheets
Table 5) Data for Six Stranded Sheets
Table 6) Data for Seven Stranded Sheets
Table 7) Data for Eight Stranded Sheets
Table 8) Data for Nine Stranded Sheets
Table 9) Data for Ten Stranded Sheets
Table 10) Data for Eleven, Twelve, Thirteen, Fourteen, and Fifteen Stranded Sheets

Identification of ß-sheet motifs in three-dimensional protein structures, using a subgraph isomorphism algorithm: an update of a 1992 study.
MSc in Information Management, 1998/1999
Electronic Dissertations Library
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