The Role of Energy Minimization in Simulation Strategies of Biomolecular Systems

  • D. H. J. Mackay
  • A. J. Cross
  • A. T. Hagler


It is now possible to calculate the classical energy of a complex system such as a protein as a function of its coordinates. By making many such calculations for various coordinate values, one can explore multidimensional energy surfaces. These energy surfaces are the basis for molecular dynamics and Monte Carlo studies. Another important method for exploring these energy surfaces is to find configurations for which the energy is a minimum. By this, we mean finding a point in configuration space where all of the forces on the atoms are balanced. By simply minimizing the energy of a molecule, we can identify stable conformations. Perhaps more importantly, by adding external to the molecule in the form of restraints and constraints, a wide range of modeling strategies can be developed using minimization techniques as the foundation to answer specific questions. For example, by forcing specific atoms to overlap atoms in a template structure during a molecular geometry minimization, one can answer the question, “how much energy is required for one molecule to adopt the shape of another.” In this chapter, we discuss how minimization techniques are used in a variety of molecular strategies, focusing on the use of constraints and restraints to extend the scope and utility of traditional structure minimization.


Energy Minimization Conjugate Gradient Line Search Steep Descent Target Function 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Plenum Press, New York 1989

Authors and Affiliations

  • D. H. J. Mackay
    • 1
  • A. J. Cross
    • 1
  • A. T. Hagler
    • 1
    • 2
  1. 1.Biosym Technologies, Inc.San DiegoUSA
  2. 2.Agouron InstituteLa JollaUSA

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