AN INTRODUCTION TO COMPUTATIONAL BIOCHEMISTRY - C. Stan Tsai.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
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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,
fax (978) 750-4744. Requests to the Publisher for permission should be addressed to the Permissions
Department, John Wiley & Sons, Inc., 605 Third Avenue, New York, NY 10158-0012, (212) 850-6011, fax
(212) 850-6008, E-Mail: PERMREQ WILEY.COM.
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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