• формат pdf
  • размер 5.33 МБ
  • добавлен 12 июля 2011 г.
Becker O.M., MacKerell A.D., Roux B., Watanabe M. (ed.) Computational Biochemistry and BioPhysics
Marcel Dekker, Inc. 2001. - 512 p.
This book is organized so that nonspecialists as well as more advanced users can benefit. It can serve as both an introductory text to computational biology, making it useful for students, and a reference source for active researchers in the field. We have tried to compile a comprehensive but reasonably concise review of relevant theoretical and computational methods that is self-contained. Therefore, the chapters, particularly in Part I, are ordered so that the reader can easily follow from one topic to the next and be systematically introduced to the theoretical methods used in computational studies of biomolecular systems. The remainder of the book is designed so that the individual parts as well as their chapters can be read independently. Additional technical details can be found in the references listed in each chapter. Thus the book may also serve as a useful reference for both theoreticians and experimentalists in all areas of biophysics and biochemical research.
This volume thus presents a current and comprehensive account of computational methods and their application to biological macromolecules. We hope that it will serve as a useful tool to guide future investigations of proteins, nucleic acids, and biological membranes, so that the mysteries of biological molecules can continue to be revealed.

Contents

Foreword Martin Karplus

Preface

Contributors

Part I Computational Methods

Introduction

Oren M. Becker, Alexander D. MacKerell, Jr., Beno??t Roux, and
Masakatsu Watanabe

Atomistic Models and Force Fields
Alexander D. MacKerell, Jr.

Dynamics Methods
Oren M. Becker and Masakatsu Watanabe

Conformational Analysis
Oren M. Becker

Treatment of Long-Range Forces and Potential
Thomas A. Darden

Inteal Coordinate Simulation Method
Alexey K. Mazur

Implicit Solvent Models
Beno??t Roux

Normal Mode Analysis of Biological Molecules
Steven Hayward

Free Energy Calculations
Thomas Simonson

Reaction Rates and Transition Pathways
John E. Straub

Computer Simulation of Biochemical Reactions with QM–MM Methods
Paul D. Lyne and Owen A. Walsh

Part II Experimental Data Analysis

X-Ray and Neutron Scattering as Probes of the Dynamics of Biological Molecules

Jeremy C. Smith

Applications of Molecular Modeling in NMR Structure Determination
Michael Nilges

Part III Modeling and Design

Comparative Protein Structure Modeling

Andra?s Fiser, Roberto Sa?nchez, Francisco Melo, and Andrej S ? ali

Bayesian Statistics in Molecular and Structural Biology
Roland L. Dunbrack, Jr.

Computer Aided Drug Design
Alexander Tropsha and Weifan Zheng

Part IV Advanced Applications

Protein Folding: Computational Approaches
Oren M. Becker

Simulations of Electron Transfer Proteins
Toshiko Ichiye

The RISM-SCF/MCSCF Approach for Chemical Processes in Solutions
Fumio Hirata, Hirofumi Sato, Seiichiro Ten-no, and Shigeki Kato

Nucleic Acid Simulations
Alexander D. MacKerell, Jr. and Lennart Nilsson

Membrane Simulations
Douglas J. Tobias

Appendix: Useful Inteet Resources

Index
Смотрите также

Atwood T., Campbell P., Parish H. et al. Oxfоrd Dictionary of Biochemistry and Molecular Biology

  • формат pdf
  • размер 7.5 МБ
  • добавлен 17 августа 2011 г.
Oxfоrd Univеrsity Prеss, 2006. - 736 pages. Second Edition. The Oxfоrd Dictionary of Biochemistry and Molecular Biology provides a comprehensive survey of current biochemistry and molecular biology. Over the last few years, the language of Biochemistry and Molecular Biology has expanded enormously to the extent that few scientists can expect to be familiar with all aspects of it. This is partly due to the Genome projects and the successive -omic...

Drenth J. Principles of Protein X-Ray Crystallography

  • формат pdf
  • размер 4.28 МБ
  • добавлен 03 октября 2011 г.
Springer Science+Business Media; 3rd edition, 2007, 332 pages Springer Advanced Texts in Chemistry X-ray crystallography has long been a vital method for studying the structure of proteins and other macromolecules. As the importance of proteins continues to grow, in fields from biochemistry and biophysics to pharmaceutical development and biotechnology, many researchers have found that a knowledge of X-ray diffraction is an indispensable tool....

G?bor N?ray-Szab?, Arieh Warshel. Computational Approaches to Biochemical Reactivity. Understanding chemical reactivity (Volume 19)

  • формат pdf
  • размер 6.87 МБ
  • добавлен 12 февраля 2011 г.
Издатель: Springer, 2002 ISBN 140200415X, 9781402004155 Количество страниц: 392 This book summarises recent results in the rapidly developing discipline of the computational aspects of biochemical reactivity. It presents a comprehensive and critical treatise on the subject, with numerous references covering practically all relevant and recent work. The chapters, written by eminent experts in the field, deal with quantum mechanical models for rea...

Hiram F. Gilbert. Basic concepts in biochemistry. A students survival guide

  • формат pdf
  • размер 6.33 МБ
  • добавлен 29 октября 2011 г.
Second edition. 2000, by the McGraw-Hill Companies. 311 p. This book presents what are often viewed as the more difficult concepts in an introductory biochemistry.

Lippincott Williams. Lippincott Illustarted Review. Biochemistry Ed 3

  • формат pdf
  • размер 127.66 МБ
  • добавлен 15 мая 2011 г.
Publisher: Lippincott Williams & Wilkins; Third edition (July 30, 2004) Language: English ISBN-10: 0781722659 ISBN-13: 978-0781722650 Lippincott’s Illustrated Reviews: Biochemistry has been the best-selling medical-level biochemistry review book on the market for the past ten years. The book is beautifully designed and executed, and renders the study of biochemistry enormously appealing to medical students and various allied health students....

Moore J.T., Langley R. Biochemistry For Dummies

  • формат pdf
  • размер 11.17 МБ
  • добавлен 24 января 2012 г.
Wiley, 2008. - 362. - This friendly, unintimidating guide presents an overview of the material covered in a typical college-level biochemistry course and makes the subject easy to understand and accessible to everyone. From cell ultrastructure and carbohydrates to amino acids, proteins, and supramolecular structure, you'll identify biochemical structures and reactions, and send your grades soaring. Newest biology, biochemistry, chemistry, and sc...

Moran L.A., Horton H.R., Scrimgeour K.G., Perry M.D. Principles of Biochemistry (Fifth Edition)

  • формат pdf
  • размер 83.93 МБ
  • добавлен 28 января 2012 г.
Pearson Education, Inc., 2012. - 824 p. - Principles of Biochemistry provides a concise introduction to fundamental concepts of biochemistry, striking the right balance of rigor and detail between the encyclopedic volumes and the cursory overview texts available today. Widely praised for accuracy, currency, and clarity of exposition, the Fifth Edition offers a new student-friendly design, an enhanced visual program, new Application Boxes, contemp...

Oren M. Becker, Alexander D. MacKerell, Jr., Benoit Roux, Masakatsu Watanabe. Computational Biochemistry and Biophysics

  • формат pdf
  • размер 5.9 МБ
  • добавлен 12 февраля 2011 г.
Издатель: CRC Press, 2001 ISBN 0824741404, 9780824741402 Всего страниц: 512 The book provides the needed information for calculating and interpreting experimentally observed properties on the basis of the results generated by computer simulations. This book is organized so that nonspecialists as well as more advanced users can benefit. It can serve as both an introductory text to computational biology, making it useful for students, and a refere...

Tsai C.S. An introduction to computational biochemistry

  • формат pdf
  • размер 7.39 МБ
  • добавлен 22 декабря 2011 г.
John Wiley & Sons, Inc., 2002, - 371 pages. This book delves into practical solutions to biochemical problems with software programs and interactive bioinformatics found on the World Wide Web. After the introduction in Chapter 1, the concept of biochemical data analysis and management is described in 2nd Chapter. The interactions between biochemists and computers are the topics of Chapter 3 (Internet resources) and Chapter 4 (computer graphi...

Vance D.E., Vance J.E. (eds.) Biochemistry of Lipids, Lipoproteins and Membranes

  • формат pdf
  • размер 68.25 МБ
  • добавлен 28 мая 2011 г.
4th ed. Elsevier. 2002. 624 p. The first edition of this book was published in 1985. The content of the 4th edition reflects the enormous advances that have occurred since that time in the field of lipid biochemistry. This publication is unique in that it represents a bridge between the superficial coverage of the lipid field found in basic biochemistry text books and the highly specialized material contained in scientific review articles and mo...