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Computation of Biomolecular Structures

Achievements, Problems, and Perspectives

  • Conference proceedings
  • © 1993

Overview

Editors:
  1. Dikeos Mario Soumpasis

    1. Abt. Molekulare Biologie, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany

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  2. Thomas M. Jovin

    1. Abt. Molekulare Biologie, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany

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Table of contents (16 papers)

  1. Front Matter

    Pages I-VIII
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  2. Structure Analysis and Prediction

    1. Structure Determination from NMR — Application to Crambin

      • J. A. C. Rullmann, A. M. J. J. Bonvin, R. Boelens, R. Kaptein
      Pages 1-14

    2. From Sequence Similarity to Structural Homology of Proteins

      • Chris Sander, Reinhard Schneider
      Pages 15-28

    3. Equilibrium Distribution of Secondary Structures for Large RNA

      • J. S. McCaskill
      Pages 29-42

    4. Doing Sequence Analysis by Inspecting the Order in which Neural Networks Learn

      • S. Brunak
      Pages 43-53

    5. Computational Approaches to Nucleic Acid Structure

      • Wilma K. Olson
      Pages 55-63

    6. A New Program for the Analysis of Nucleic Acid Structure: Implications for Nucleic Acid Structure Interpretation

      • Marla S. Babcock, Wilma K. Olson
      Pages 65-85

    7. Modeling DNA Backbone Structures

      • Chang-Shung Tung
      Pages 87-97

  3. Specific Systems

    1. Serine and Cysteine Proteases and their Natural Inhibitors: Structures and Implications for Function and Drug Design

      • Robert Huber
      Pages 99-102

    2. Principles of Protein — Protein Recognition in Protease-Inhibitor and Antigen-Antibody Complexes

      • Joël Janin, Jacqueline Cherfils, Stéphane Duquerroy
      Pages 103-114

    3. Subtleties in Designing DNA Sequence Specific Ligands

      • M. Randrianarivelo, K. Zakrzewska
      Pages 115-135

    4. The Structure of DNA Four-Way Junctions

      • Eberhard von Kitzing, David M. J. Lilley, Stephan Diekmann
      Pages 137-156

  4. Physical Chemistry and Dynamics

    1. Rapid Conformational Investigations of Organic Molecules

      • Rodney M. J. Cotterill, Eric Platt, Barry Robson
      Pages 157-163

    2. Dynamics of DNA Oligomers: Harmonic and Anharmonic Motions

      • Angel E. García
      Pages 165-199

    3. Surface Boundary Conditions: A Simulation Model for Macromolecules

      • A. H. Juffer, H. J. C. Berendsen
      Pages 201-206

    4. Computation of Ionic Distributions around Charged Biomolecular Structures using the PMF Approach

      • Reinhard Klement
      Pages 207-222

    5. Formal Aspects of the Potential of Mean Force Approach

      • Dikeos Mario Soumpasis
      Pages 223-239

  5. Back Matter

    Pages 241-252
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Keywords

About this book

Computational techniques have become an indispensable part of Molecular Biology, Biochemistry, and Molecular Design. In conjunction with refined experimental methods and powerful hardware, they enable us to analyze and visualize biomolecular structures, simulate their motions and to a variable degree understand their physicochemical properties and function. In addition, they provide essentially the only way to analyze and correlate the astronomical amounts of experimental sequence and structural data accumulating in international databases. We have good reasons to believe that further advances in this area will eventually enable us to predict with sufficient accuracy many structural and functional properties of fairly large biomolecules, given their sequence and specified environmental conditions. However, it is also important to realize that in achieving this goal, we encounter several serious problems of conceptual and methodological nature, the solution of which requires new approaches and algorithms. For example, we need better force fields, more efficient optimization routines, an adequate description of electrostatics and hydration, reliable methods to compute free energies, and ways to extent the length of molecular dynamics simulations by several orders of magnitude.

Editors and Affiliations

  • Abt. Molekulare Biologie, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany

    Dikeos Mario Soumpasis, Thomas M. Jovin

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