Proteins fold in interesting and intriguing ways. Importantly, the structure of a protein can provide additional clues to its function(s) than does its sequence alone. Scientists interested in characterizing a novel protein sequence should therefore not only familiarize themselves with computer tools and methods for sequence analysis but also with those for structure analysis. Computer scientists interested in developing software tools for bioinformatics will find that structure analysis is no less interesting and challenging than sequence analysis. Both scientists and computer scientists will note that the field of protein structure analysis is going to become increasingly important in coming years, now that the post-genomic era is here.

This ebooklet is a light version of the print short book Protein Structure Informatics ISBN 0-9700297-1-3 available from http://www.amazon.com. It contains two of the seven chapters-1. Main Structure Databases, 2. Aligning A Structure to A Structure-of the print book. This ebooklet is aimed towards two audiences. Biologists with more of an interest in learning about protein structure databases than inner workings of algorithms might find this inexpensive version attractive (the print version has several chapters on algorithmic aspects of protein structure informatics as well). Computer scientists will, in addition, get a "preview" of the algorithmic aspects in the full book, in the form of one full algorithmic chapter from it ( Aligning Structures to Structures).

CONTENTS

PREFACE

MAIN STRUCTURE DATABASES
Protein Data Bank
Structure entry format
PDB from a software engineering perspective
PDB from a content perspective
Viewing structures
Structure viewers for PDB
Searching PDB
Molecular Modeling Database
File format
The CN3D structure viewer for MMDB
References

ALIGNING A STRUCTURE TO A STRUCTURE
The alignment problem formalized
Optimization methods
Various refinements
Key atoms
Polypeptide fragments
Secondary structure elements
Distance submatrices
Parallels to sequence alignment
Statistical significance of an alignment
Structure alignment tools: CE - DALI - VAST
Modeling and aligning structures with graphs
Graphs
Graphs of protein structures
Aligning structures by aligning their graphs
Exercises
References

About the Author:
Arun Jagota is a research associate at the University of California, Santa Cruz, and an adjunct faculty member in the department of applied mathematics at Santa Clara University. He has also been an adjunct faculty member at the University of California, Santa Cruz, at the University of Memphis, and at the University of North Texas. He has also taught at the University of California Berkeley, Extension, at the University of California, Santa Cruz, Extension, and at San Jose State University. He presently teaches a number of bioinformatics courses at the University of California, Santa Cruz extension, where he co-developed their national award winning certificate program in Bioinformatics. He also teaches bioinformatics courses at the University of California, Berkeley extension and remotely at the University of Birmingham, Alabama. He conducts research in bioinformatics and the allied fields of neural networks and machine learning.