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Computational Methods for Macromolecules: Challenges and Applications

Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modeling, New York, October 12–14, 2000

  • Conference proceedings
  • © 2002

Overview

Editors:
  1. Tamar Schlick

    1. Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, New York, USA
      Howard Hughes Medical Institute, New York, USA

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  2. Hin Hark Gan

    1. Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, New York, USA
      Howard Hughes Medical Institute, New York, USA

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    You can also search for this editor in PubMed   Google Scholar

Part of the book series: Lecture Notes in Computational Science and Engineering (LNCSE, volume 24)

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Table of contents (19 papers)

  1. Front Matter

    Pages I-IX
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  2. Introduction

    1. Front Matter

      Pages 1-1
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    2. Methods for Macromolecular Modeling (M3): Assessment of Progress and Future Perspectives

      • Hin Hark Gan, Tamar Schlick
      Pages 3-27

  3. Biomolecular Dynamics Applications

    1. Front Matter

      Pages 29-29
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    2. Mathematics and Molecular Neurobiology

      • Nathan A. Baker, Kaihsu Tai, Richard Henchman, David Sept, Adrian Elcock, Michael Holst et al.
      Pages 31-60

    3. Structural and Dynamical Characterization of Nucleic Acid Water and Ion Binding Sites

      • Pascal Auffinger, Benoit Masquida, Eric Westhof
      Pages 61-70

  4. Molecular Dynamics Methods

    1. Front Matter

      Pages 71-71
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    2. A Test Set for Molecular Dynamics Algorithms

      • Eric Barth, Benedict Leimkuhler, Sebastian Reich
      Pages 73-103

    3. Internal Coordinate Molecular Dynamics Based on the Spectroscopic B-Matrix

      • Sang-Ho Lee, Kim Palmo, Samuel Krimm
      Pages 104-128

    4. The Sigma MD Program and a Generic Interface Applicable to Multi-Functional Programs with Complex, Hierarchical Command Structure

      • Geoff Mann, R. H. Yun, Lars Nyland, Jan Prins, John Board, Jan Hermans
      Pages 129-145

    5. Overcoming Instabilities in Verlet-I/r-RESPA with the Mollified Impulse Method

      • Jesús A. Izaguirre, Qun Ma, Thierry Matthey, Jeremiah Willcock, Thomas Slabach, Branden Moore et al.
      Pages 146-174

  6. Other Conformational Sampling Methods

    1. Front Matter

      Pages 233-233
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    2. Hierarchical Uncoupling-Coupling of Metastable Conformations

      • Alexander Fischer, Christof Schütte, Peter Deuflhard, Frank Cordes
      Pages 235-259

    3. Automatic Identification of Metastable Conformations via Self-Organized Neural Networks

      • T. Galliat, P. Deuflhard, R. Roitzsch, F. Cordes
      Pages 260-284
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Keywords

Reviews

POLYMER NEWS

REVIEW BY ANDRZEJ KLOCZKOWSKI, BAKER CENTER FOR BIOINFORMATICS AND BIOLOGICAL STATISTICS, IOWA STATE UNIVERSITY

"The authors of the articles in the book are the top specialists in their fields and the book presents the current state of the art for the broad spectrum of all currently used methods and techniques of macromolecular modeling. The book might be very useful for all readers interested in the computational modeling of macromolecules. Several articles in the book cover different aspects of protein modeling, so I would highly recommend this book to all readers interested in modeling of proteins."

Editors and Affiliations

  • Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, New York, USA

    Tamar Schlick, Hin Hark Gan

  • Howard Hughes Medical Institute, New York, USA

    Tamar Schlick, Hin Hark Gan

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