Introduction to Computational Biochemistry - J Ramsden.pdf

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AN INTRODUCTION TO
COMPUTATIONAL
BIOCHEMISTRY
 
AN INTRODUCTION TO
COMPUTATIONAL
BIOCHEMISTRY
C. Stan Tsai, Ph.D.
Department of Chemistry
and Institute of Biochemistry
Carleton University
Ottawa, Ontario, Canada
A JOHN WILEY & SONS, INC., PUBLICATION
2632917.001.png
a
This book is printed on acid-free paper.
Copyright 2002 by Wiley-Liss, Inc., New York. All rights reserved.
Published simultaneously in Canada.
No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form
or by any means, electronic, mechanical, photocopying, recording, scanning or otherwise, except as
permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the
prior written permission of the Publisher, or authorization through payment of the appropriate per-copy
fee to the Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400,
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For orderingand customer service information please call 1-800-CALL-WILEY.
Library of Congress Cataloging-in-Publication Data:
Tsai, C. Stan.
An introduction to computational biochemistry / C. Stan Tsai.
p. cm.
Includes bibliographical references and index.
ISBN 0-471-40120-X (pbk. : alk. paper)
1. Biochemistry--Data processing. 2. Biochemistry--Computer simulation. 3.
Biochemistry--Mathematics. I. Title.
QP517.M3 T733 2002
572 .0285--dc21
2001057366
Printed in the United States of America.
10987654321
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CONTENTS
Preface . . . . . . . . . . . .................................... ix
1 INTRODUCTION
1
1.1. Biochemistry: Studies of Life at the Molecular Level . . . ......
1
1.2. Computer Science and Computational Sciences . ............
5
1.3. Computational Biochemistry: Application of Computer
Technology to Biochemistry ............................
6
References . . . . . ........................................
9
2 BIOCHEMICAL DATA: ANALYSIS AND
MANAGEMENT 11
2.1. Statistical Analysis of Biochemical Data . . . . . . ............ 11
2.2. Biochemical Data Analysis with Spreadsheet Application ..... 20
2.3. Biochemical Data Management with Database Program ...... 28
2.4. Workshops . ........................................ 31
References . . . . . ........................................ 40
3 BIOCHEMICAL EXPLORATION: INTERNET RESOURCES 41
3.1. Introduction to Internet . .............................. 41
3.2. Internet Resources of Biochemical Interest . . . . . ............ 46
3.3. Database Retrieval ................................... 48
3.4. Workshops . ........................................ 52
References . . . . . ........................................ 52
4 MOLECULAR GRAPHICS: VISUALIZATION OF
BIOMOLECULES 53
4.1. Introduction to Computer Graphics . . . . . . . . . ............ 53
4.2. Representation of Molecular Structures . . . . . . . ............ 56
4.3. Drawingand Display of Molecular Structures . . ............ 60
4.4. Workshops . ........................................ 69
References . . . . . ........................................ 70
v
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vi
CONTENTS
5 BIOCHEMICAL COMPOUNDS: STRUCTURE AND
ANALYSIS 73
5.1. Survey of Biomolecules . .............................. 73
5.2. Characterization of Biomolecular Structures . . . ............ 80
5.3. Fittingand Search of Biomolecular Data and Information .... 87
5.4. Workshops . ........................................ 98
References . . . . . ........................................ 103
6 DYNAMIC BIOCHEMISTRY: BIOMOLECULAR
INTERACTIONS 107
6.1. Biomacromolecule — Ligand Interactions . . . . . . . ............ 107
6.2. Receptor Biochemistry and Signal Transduction ............ 111
6.3. Fittingof BindingData and Search for Receptor Databases . . . 113
6.4. Workshops . ........................................ 119
References . . . . . ........................................ 121
7 DYNAMIC BIOCHEMISTRY: ENZYME KINETICS 123
7.1. Characterization of Enzymes . . . ........................ 123
7.2. Kinetics of Enzymatic Reactions ........................ 126
7.3. Search and Analysis of Enzyme Data . . . . . . . . . ............ 133
7.4. Workshops . ........................................ 140
References . . . . . ........................................ 144
8 DYNAMIC BIOCHEMISTRY: METABOLIC SIMULATION 147
8.1. Introduction to Metabolism ............................ 147
8.2. Metabolic Control Analysis ............................ 152
8.3. Metabolic Databases and Simulation . . . . . . . . . ............ 153
8.4. Workshops . ........................................ 160
References . . . . . ........................................ 162
9 GENOMICS: NUCLEOTIDE SEQUENCES AND
RECOMBINANT DNA
165
9.1. Genome, DNA Sequence, and Transmission of Genetic
Information ........................................ 165
9.2. Recombinant DNA Technology . ........................ 169
9.3. Nucleotide Sequence Analysis . . ........................ 171
9.4. Workshops . ........................................ 179
References . . . . . ........................................ 181

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