Computer Simulation of Biomolecular Systems

1. Front Matter

   Pages i-xxvi

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2. Methodology

   1. Front Matter

      Pages 1-1

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   2. Empirical classical interaction functions for molecular simulation

      • P. H. Hünenberger, W. F. van Gunsteren

      Pages 3-82

   3. The development/application of a ‘minimalist’ organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data

      • Peter Kollman, Richard Dixon, Wendy Cornell, Thomas Fox, Chris Chipot, Andrew Pohorille

      Pages 83-96

   4. A separating framework for increasing the timestep in molecular dynamics

      • Eric Barth, Margaret Mandziuk, Tamar Schlick

      Pages 97-121

   5. Reduced variable molecular dynamics

      • James Turner, Paul K. Weiner, Barry Robson, Ravi Venugopal, Harry Schubele III, Ramen Singh

      Pages 122-149

   6. Gaussian shape methods

      • J. A. Grant, B. T. Pickup

      Pages 150-176

   7. Systematic procedure for the development of accurate QM/MM model Hamiltonians

      • Mark A. Cunningham, Paul A. Bash

      Pages 177-195

3. Electrostatics and solvation

   1. Front Matter

      Pages 197-197

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   2. Modeling protonation equilibria in biomolecules

      • Michael K. Gilson

      Pages 199-222

   3. Semi-explicit bag model for protein solvation

      • Richard C. Brower, S. Roy Kimura

      Pages 223-243

   4. Application of Poisson—Boltzmann solvation forces to macromolecular simulations

      • Adrian H. Elcock, Michael J. Potter, J. Andrew McCammon

      Pages 244-261

4. Structure refinement

   1. Front Matter

      Pages 263-263

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   2. Time-averaging crystallographic refinement

      • Celia A. Schiffer

      Pages 265-269

   3. Incorporation of solvation energy contributions for energy refinement and folding of proteins

      • Werner Braun

      Pages 270-283

   4. Normal mode analysis of biomolecular dynamics

      • David A. Case

      Pages 284-301

5. Simulation of large systems

   1. Front Matter

      Pages 303-303

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   2. Dynamics of biomolecules: Simulation versus X-ray, neutron and infrared experiment

      • Jeremy C. Smith

      Pages 305-360

6. Protein folding

   1. Front Matter

      Pages 361-361

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   2. Protein structure prediction by global energy optimization

      • Ruben A. Abagyan

      Pages 363-394

The third volume in the series on Computer Simulation of Biomolecular Systems continues with the format introduced in the first volume [1] and elaborated in the second volume [2]. The primary emphasis is on the methodological aspects of simulations, although there are some chapters that present the results obtained for specific systems of biological interest. The focus of this volume has changed somewhat since there are several chapters devoted to structure-based ligand design, which had only a single chapter in the second volume. It seems useful to set the stage for this volume by quoting from my preface to Volume 2 [2]. "The long-range 'goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last fifty years great progress has been made in applying the equations representing the underlying physical laws to chemical problems involv­ ing the structures and reactions of small molecules. Corresponding studies of mesoscopic systems have been undertaken much more recently. Molecular dynamics simulations, which are the primary focus of this volume, represent the most important theoretical approach to macromolecules of biological interest." ...

• Dynamics
• Potential
• X-ray
• computer simulation
• development
• experiment
• protein
• simulation

• Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Zentrum, Zürich, Switzerland

  Wilfred F. Gunsteren

• Amdyn Systems Inc., Somerville, USA

  Paul K. Weiner

• Zeneca Pharmaceuticals, Cheshire, UK

  Anthony J. Wilkinson

Policies and ethics