Protein Structure Informatics

by Jagota, Arun K.

• ISBN13: 9780970029713
• ISBN10: 0970029713
• Edition: 1st
• Format: Paperback
• Copyright: 2005-06-30
• Publisher: Bioinformatics by the Bay

Summary

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 short book introduces the topic of protein structure informatics in two parts. Part I covers the main public-domain protein structure databases, and associated tools such as structure viewers and search tools. Part II covers problems and algorithms for aligning a structure to a structure, a sequence to a structure, for predicting a structure for a sequence, on "protein structure profiles", and the molecular docking problem. All chapters contain references for further reading. This book has been cooking slowly for more than two years. Over this period, it has undergone numerous revisions and refinements. The material has also been presented and refined in classes taught by the author at the University of California, Santa Cruz extension.

Author Biography

Arun Jagota is a PhD in computer science from The State University of New York at Buffalo. He teaches courses in bioinformatics at the University of California, Santa Cruz extension, and has taught courses in computer science at the University of California, Santa Cruz for a number of years. He is also adjunct faculty at Santa Clara University, where he teaches computer science and applied math courses. He has also taught at San Jose State University. He has been a visiting faculty member at the University of Memphis and at the University of North Texas. He has taught more than thirty five different courses in computer science, and some in mathematics. He has authored more than twenty research papers in journals, and about the same number in conference records. He conducts research in machine learning and in bioinformatics.