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Computer Simulations of Protein Structures and Interactions

  • Book
  • © 1995

Overview

Authors:
  1. S. Fraga

    1. Department of Chemistry, University of Alberta, Edmonton, Canada
      Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, Canto Blanco (Madrid), Spain

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  2. J. M. R. Parker

    1. Alberta Peptide Institute and Department of Biochemistry, University of Alberta, Edmontom, Canada

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    You can also search for this author in PubMed   Google Scholar

  3. J. M. Pocock

    1. Department of Biochemistry, University of Dundee, Dundee, Scotland, UK

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    You can also search for this author in PubMed   Google Scholar

Part of the book series: Lecture Notes in Chemistry (LNC, volume 66)

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Table of contents (12 chapters)

  1. Front Matter

    Pages I-XII
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  2. Introduction

    1. Introduction

      • S. Fraga, J. M. R. Parker, J. M. Pocock
      Pages 1-2

  3. Protein Folding

    1. Front Matter

      Pages 3-3
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    2. Amino Acids, Peptides, and Proteins

      • S. Fraga, J. M. R. Parker, J. M. Pocock
      Pages 4-25

  4. Theoretical Formulation

    1. Front Matter

      Pages 26-26
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    2. Quantum Mechanics

      • S. Fraga, J. M. R. Parker, J. M. Pocock
      Pages 27-57

    3. Statistical Mechanics

      • S. Fraga, J. M. R. Parker, J. M. Pocock
      Pages 58-70

    4. Molecular Mechanics: The Potential Energy Function

      • S. Fraga, J. M. R. Parker, J. M. Pocock
      Pages 71-97

    5. Molecular Mechanics: Computer Simulations

      • S. Fraga, J. M. R. Parker, J. M. Pocock
      Pages 98-127

    6. Practical Overview

      • S. Fraga, J. M. R. Parker, J. M. Pocock
      Pages 128-129

  5. Experimental and Theoretical Data

    1. Front Matter

      Pages 130-130
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    2. Databases

      • S. Fraga, J. M. R. Parker, J. M. Pocock
      Pages 131-138

  6. Modeling of Isolated Systems and Associations

    1. Front Matter

      Pages 139-139
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    2. Prediction of Secondary Structures

      • S. Fraga, J. M. R. Parker, J. M. Pocock
      Pages 140-163

    3. Modeling of Tertiary Structures

      • S. Fraga, J. M. R. Parker, J. M. Pocock
      Pages 164-195

    4. Molecular Associations

      • S. Fraga, J. M. R. Parker, J. M. Pocock
      Pages 196-213

  7. Applications

    1. Front Matter

      Pages 214-214
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    2. Structure-Aided Molecular Design

      • S. Fraga, J. M. R. Parker, J. M. Pocock
      Pages 215-234

  8. Back Matter

    Pages 235-284
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Keywords

About this book

Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.

Authors and Affiliations

  • Department of Chemistry, University of Alberta, Edmonton, Canada

    S. Fraga

  • Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, Canto Blanco (Madrid), Spain

    S. Fraga

  • Alberta Peptide Institute and Department of Biochemistry, University of Alberta, Edmontom, Canada

    J. M. R. Parker

  • Department of Biochemistry, University of Dundee, Dundee, Scotland, UK

    J. M. Pocock

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